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

Nonomuraea sediminis sp. nov., a novel actinobacterium with antimicrobial activity, isolated from sediment of Dianchi Lake

A novel actinobacterium with antimicrobial activity, designated strain H16431^T, was isolated from a sediment sample collected from Dianchi Lake, Yunnan Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain H16431^T was most closely related to Nonomuraea rhizosphaerae CGMCC 4.7431^T and Nonomuraea guangzhouensis CGMCC 4.7101^T (98.1% similarity), but formed a monophyletic clade with Nonomuraea ceibae KCTC 39826^T (98.0% similarity). Phylogenomic analysis based on whole-genome sequence showed that strain H16431^T formed a separate clade within the genus Nonomuraea. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between strain H16431^T and its closely related Nonomuraea species were 80.0-81.5%, 71.2-74.6%, and 23.2-25.0%, respectively, which were significantly lower than the widely accepted species-defined threshold. The DNA G + C content was 70.2% based on the whole-genome sequence. The menaquinones were identified as MK-9(H₄), MK-9(H₆), and MK-9(H₂). The major fatty acids were iso-C_16:0, 10 methyl-C_17:0, and iso-C_16:0 2OH. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, and phosphatidylinositol. These chemotaxonomic characteristics were corresponded to those of the genus Nonomuraea. On the basis of the taxonomic evidence, strain H16431^T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea sediminis sp. nov. is proposed. The type strain is H16431^T (=JCM 34852^T=CICC 25119^T).

Radiobacillus kanasensis sp. nov., a halotolerant bacterium isolated from woodland soil

A novel Gram-positive, aerobic, rod-shaped, non-motile, endospore-forming salt-tolerant bacterium strain (80^T), was isolated from woodland soil collected near Kanas lake in the Altay region of Xinjiang, PR China. The strain grew at 15-45 °C, pH6.0-9.0 and with 0-14 % (w/v) NaCl. The complete genome size of the novel strain was 4 031 766 bp including a circle chromosome and a circle plasmid. The genomic DNA G+C content was 38.99 mol %. Phylogenetic analysis based on 16S rRNA gene sequence and genome showed that strain 80^T has the highest similarity to Radiobacillus deserti TKL69^T. However, the novel strain showed an average nucleotide identity value of 78.65 % (lower than 95 %) and a digital DNA-DNA hybridization value of 22.30 % with R. deserti TKL69^T based on the genome sequences. The major fatty acids were anteiso-C_15 : 0, iso-C_15 : 0, anteiso-C_17:0 and C_16 : 1 ω7c alcohol. The only respiratory quinone was MK-7. The cell wall peptidoglycan was meso-diaminopimelic acid. Diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid, one unidentified aminophospholipid and two unidentified glycolipids were identified as the major polar lipids. The phylogenetic, phenotypic and chemotaxonomic analyses showed that strain 80^T represents a novel species of the genus Radiobacillus and the name Radiobacillus kanasensis sp. nov. is proposed. The type strain is 80^T (=GDMCC 1.2844^T=JCM 35077^T).

Actinobacteria From Desert: Diversity and Biotechnological Applications

Deserts, as an unexplored extreme ecosystem, are known to harbor diverse actinobacteria with biotechnological potential. Both multidrug-resistant (MDR) pathogens and environmental issues have sharply raised the emerging demand for functional actinobacteria. From 2000 to 2021, 129 new species have been continuously reported from 35 deserts worldwide. The two largest numbers are of the members of the genera Streptomyces and Geodermatophilus, followed by other functional extremophilic strains such as alkaliphiles, halotolerant species, thermophiles, and psychrotolerant species. Improved isolation strategies for the recovery of culturable and unculturable desert actinobacteria are crucial for the exploration of their diversity and offer a better understanding of their survival mechanisms under extreme environmental stresses. The main bioprospecting processes involve isolation of target actinobacteria on selective media and incubation and selection of representatives from isolation plates for further investigations. Bioactive compounds obtained from desert actinobacteria are being continuously explored for their biotechnological potential, especially in medicine. To date, there are more than 50 novel compounds discovered from these gifted actinobacteria with potential antimicrobial activities, including anti-MDR pathogens and anti-inflammatory, antivirus, antifungal, antiallergic, antibacterial, antitumor, and cytotoxic activities. A range of plant growth-promoting abilities of the desert actinobacteria inspired great interest in their agricultural potential. In addition, several degradative, oxidative, and other functional enzymes from desert strains can be applied in the industry and the environment. This review aims to provide a comprehensive overview of desert environments as a remarkable source of diverse actinobacteria while such rich diversity offers an underexplored resource for biotechnological exploitations.

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 5K548^T, 7K502^T, 16K309^T and 16K404^T, 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 5K548^T, 7K502^T, 16K404^T and 16K309^T 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 KC333^T, 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 CH32^T (99.0% sequence similarity), Nonomuraea maritima FXJ7.203 ^T (98.9%), Nonomuraea candida HMC10^T (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 KC333^T and close relatives demonstrated that it represents a novel species of the genus Nonomuraea. The major cellular fatty acids of strain KC333^T were iso-C_16: 0, C_17:0 10-methyl and iso-C_16: 0 2OH. Strain KC333^T 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 KC333^T 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 KC333^T (= DSM 107062 ^T = JCM 32584 ^T = KCTC 49111 ^T) as the type strain.

Nonomuraea cypriaca sp. nov., isolated from soil

A novel actinobacterium, designated strain K274^T, was isolated from soil collected from Zafer Cape (Cape Apostolos Andreas), the easternmost tip of Cyprus on the Karpas peninsula, Magusa, Northern Cyprus, and a polyphasic approach was used for characterization of the strain. The isolate was found to have chemotaxonomic and morphological properties associated with members of the genus Nonomuraea. The strain has the highest similarity to Nonomuraea zeae DSM 100528^T with 99.1% similarity value. In the phylogenetic dendogram based on 16S rRNA gene sequence, strain K274^T was formed a distinct clade together N. zeae DSM 100528^T, 'Nonomuraea basaltis' 160415 (98.9% similarity), and 'Nonomuraea lycopersici' NEAU-DE8(1) (98.2% similarity). The genome sequence of strain K274^T was 11.5 Mbp in size with a total of 11,848 protein-coding genes and 75 RNA genes. The genomic G + C content of the novel strain was 69.7 mol%. Both average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) results between the strain and phlyogenetic neighbours were well below the threshold value, and the novelty are supported by phenotypic and chemotaxonomic differences. Because of all these, strain K274^T represents a novel species in the genus Nonomuraea, for which the name Nonomuraea cypriaca sp. nov. is proposed. The type strain is K274^T (= DSM 45718^T = KCTC 29095^T).

Nonomuraea antri sp. nov., an actinomycete isolated from cave soil in Thailand

A novel actinobacterium, designated strain NN258T, was isolated from a cave soil sample collected from a karst cave at Khao No-Khao Kaeo, Nakhon Sawan province, Thailand. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Nonomuraea . Strain NN258T showed the highest 16S rRNA gene sequence similarity values to Nonomuraea candida HMC10T, Nonomuraea mesophila 6K102T, Nonomuraea rubra DSM 43768T, Nonomuraea diastatica KC712T and Nonomuraea helvata IFO 14681T. The strain formed an extensively branched substrate and aerial mycelia. The whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid, with glucose, madurose, mannose and ribose as the whole-cell sugars. The polar lipids were diphosphatidylglycerol, phosphotidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylmonomethylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, two unidentified phospholipids, three unidentified sugar-containing phosphoaminolipids, an unidentified glycolipid and two unidentified lipids. The predominant menaquinone was MK-9(H4), with minor amounts of MK-9(H0), MK-9(H2) and MK-9(H6). Major cellular fatty acids (>10%) were iso-C16 : 0 and 10-methyl-C17 : 0. The G+C content of the genomic DNA was 71.0 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain NN258T and the reference strains were 79.9–80.9 % and 26.1–27.0 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain NN258T represents a novel species of the genus Nonomuraea , for which the name Nonomuraea antri sp. nov. is proposed. The type strain is NN258T (=TBRC 11478T=NBRC 114269T).

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 160415^T, 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 160415^T clustered closely with species of the genus Nonomuraea, and showed the highest sequence similarity to Nonomuraea zeae NEAU-ND5^T, Nonomuraea candida HMC10^T and Nonomuraea turkmeniaca DSM 43926^T 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 160415^T 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 160415^T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea basaltis sp. nov. is proposed. The type strain is 160415^T (= KCTC 39875^T = DSM 104309^T).