To assess the diversity of actinobacterial taxa in desert sands and obtain the novel microbial resources, 79 and 50 samples were collected from the Badain Jaran (BJD) and Tengger Deserts (TGD) of China, respectively. High-throughput sequencing (HTS) of environmental 16S rRNA genes within these samples was conducted on an Illumina Miseq platform, using universal bacterial primers targeting the V3–V4 hypervariable region. Based on the HTS analyses, cultivation-dependent (CULD) techniques were optimized to identify the cultivable Actinobacteria members. A total of 346,766 16S rRNA gene reads comprising 3,365 operational taxonomic units (OTUs) were obtained from the BJD sands using HTS, while 170,583 reads comprising 1,250 OTUs were detected in the TGD sands. Taxonomic classification indicated that Actinobacteria was the predominant phylum, comprising 35.0 and 29.4% of the communities in BJD and TGD sands, respectively. Among the Actinobacteria, members of the Geodermatophilaceae were considerably abundant in both deserts, indicating that they represent ubiquitous populations within the deserts. At the genus level, Arthrobacter spp. and Kocuria spp. were dominant, and corresponded to 21.2 and 5.3% of the actinobacterial communities in BJD and TGD deserts, respectively. A total of 786 and 376 actinobacterial strains were isolated and identified from BJD and TGD samples, respectively. The isolates comprised 73 genera of 30 families within the phylum Actinobacteria. In addition to the Geodermatophilaceae, Streptomyces spp. were a prominent component of the isolates, comprising 25% of the isolates from BJD and 17.5% of those from TGD. Comparison of the actinobacterial community structure in other ecosystems indicated that Geodermatophilaceae was the main actinobacterial group in desert sands, which is consistent with our results. Additionally, in these desert habits, Geodermatophilaceae and some other core groups may promote or inhabit the subsequent members' occurrence or prosper to shape the bacteria community structure. However, it should be noted that a number of other low-abundance bacteria appear to be specific to desert sands, which are worth further investigation. In antimicrobial activity assays, 10.36 % of the tested isolates showed antimicrobial activities in one or more screens. Importantly, 37 of the newly isolated strains reported here represent novel taxa that could be valuable resources for further research of novel secondary metabolites and their ecological significance in deserts.

A novel actinobacterial strain, designated CPCC 201356^T, was isolated from a rhizosphere soil sample of the medicinal plantAstragalus membranaceusand subjected to a polyphasic taxonomic analysis. Good growth occurred at 20–32 °C, at pH 7.0–7.5 and with 0–1 % (w/v) NaCl. Colonies on R2A and ISP 2 agar were light red to red, round and lacked aerial mycelium; cells adhered to the agar. The peptidoglycan containedmeso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinones were MK-9(H₄) and MK-9. Polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and two unknown phospholipids. The major cellular fatty acids were iso-C_16 : 0, iso-C_15 : 0and C_17 : 1ω8c. The G+C content of the genomic DNA was 72.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CPCC 201356^Tbelonged to the familyGeodermatophilaceaeand consistently formed a distinct sub-branch withGeodermatophilus obscurusDSM 43160^T. The organism showed 16S rRNA gene sequence similarity of 97.7 % withG. obscurusDSM 43160^T. DNA–DNA hybridization between strain CPCC 201356^TandG. obscurusDSM 43160^Twas 17.4 %. On the basis of evidence from this polyphasic taxonomic study, a novel species,Geodermatophilus rubersp. nov., is proposed; the type strain is CPCC 201356^T(=DSM 45317^T=CCM 7619^T).

A rod- or coccus-shaped, non-spore-forming actinobacterium, designated strain SC8A-24^T, was isolated from a soil sample collected from the rhizosphere of Alhagi sparsifolia on the southern edge of the Taklimakan desert, Xinjiang, China, and examined by a polyphasic approach to clarify its taxonomic position. This actinobacterium was Gram-staining-positive and aerobic. Substrate and aerial mycelia were not observed, and no diffusible pigments were observed on the media tested. Strain SC8A-24^T grew optimally without NaCl at 28–30 °C and pH 7.0–8.0. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain SC8A-24^T belonged to the genus Nocardioides and shared the highest 16S rRNA gene sequence similarity with Nocardioides salarius CL-Z59^T (96.51 %), N. pyridinolyticus OS4^T (96.43 %) and N. ginsengagri BX5-10^T (96.37 %). The DNA G+C content of strain SC8A-24^T was 71 mol%. The cell-wall peptidoglycan contained ll-2,6-diaminopimelic acid, and MK-8(H₄) was the predominant menaquinone. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. The major fatty acids were C_17 : 1ω8c, 10-methyl C_17 : 0 and C_18 : 1ω9c. On the basis of phylogenetic analysis and phenotypic and chemotaxonomic characteristics, strain SC8A-24^T represents a novel species of the genus Nocardioides , for which the name Nocardioides deserti sp. nov. is proposed. The type strain is SC8A-24^T ( = DSM 26045^T = CGMCC 4.7183^T).

Solirubrobacter spp. were abundant in soil samples collected from deserts and other areas with high UV radiation. In addition, a novel Solirubrobacter species, with strain CPCC 204708^T as the type, was isolated and identified from sandy soil sample collected from the Badain Jaran Desert of the Inner Mongolia autonomous region. Strain CPCC 204708^T was Gram-stain positive, rod-shaped, non-motile, non-spore-forming, and grew optimally at 28–30°C, pH 7.0–8.0, and in the absence of NaCl. Analysis of the 16S rRNA gene sequence of strain CPCC 204708^T showed its identity within the genus Solirubrobacter, with highest nucleotide similarities (97.4–98.2%) to other named Solirubrobacter species. Phylogenetic and genomic analyses indicated that the strain was most closely related to Solirubrobacter phytolaccae KCTC 29190^T, while represented a distinct species, as confirmed from physiological properties and comparison. The name Solirubrobacter deserti sp. nov. was consequently proposed, with CPCC 204708^T (= DSM 105495^T = NBRC 112942^T) as the type strain. Genomic analyses of the Solirubrobacter spp. also suggested that Solirubrobacter sp. URHD0082 represents a novel species, for which the name Candidatus “Solirubrobacter pratensis” sp. nov. was proposed. Genomic analysis of CPCC 204708^T revealed the presence of genes related to its adaptation to the harsh environments of deserts and may also harbor genes functional in plant-microbe interactions. Pan-genomic analysis of available Solirubrobacter spp. confirmed the presence of many of the above genes as core components of Solirubrobacter genomes and suggests they may possess beneficial potential for their associate plant and may be important resources for bioactive compounds.

The goal of this study was to gain insight into the diversity of culturable actinobacteria in desert soil crusts and to determine the physiological characteristics of the predominant actinobacterial group in these crusts. Culture-dependent method was employed to obtain actinobacterial strains from desert soil samples collected from Shapotou National Desert Ecological Reserve located in Tengger Desert, China. A total of 376 actinobacterial strains were isolated and 16S rRNA gene sequences analysis indicated that these isolates belonged to 29 genera within 18 families, among which the members of the family Geodermatophilaceae were predominant. The combination of 16S rRNA gene information and the phenotypic data allowed these newly-isolated Geodermatophilaceae members to be classified into 33 “species clusters”, 11 of which represented hitherto unrecognized species. Fermentation broths from 19.7% of the isolated strains showed activity in at least one of the six screens for antibiotic activity. These isolates exhibited bio-diversity in enzymatic characteristics and carbon utilization profiles. The physiological characteristics of the isolates from different types of crusts or bare sand samples were specific to their respective micro-ecological environments. Our study revealed that members of the family Geodermatophilaceae were ubiquitous, abundant, and diverse in Shapotou National Desert Ecological Reserve, and these strains may represent a new major group of potential functional actinobacteria in desert soil.

Mycobacterium species exhibit high bioremediation potential for the degradation of polycyclic aromatic hydrocarbons (PAHs) that are significant environmental pollutants. In this study, three Gram-positive, rapidly growing strains (YC-RL4^T, MB418^T, and HX176^T) were isolated from petroleum-contaminated soils and were classified as Mycobacterium within the family Mycobacteriaceae. Genomic average nucleotide identity (ANI; < 95%) and digital DNA–DNA hybridization (dDDH; < 70%) values relative to other Mycobacterium spp. indicated that the strains represented novel species. The morphological, physiological, and chemotaxonomic characteristics of the isolates also supported their affiliation with Mycobacterium and their delineation as novel species. The strains were identified as Mycobacterium adipatum sp. nov. (type strain YC-RL4^T = CPCC 205684^T = CGMCC 1.62027^T), Mycobacterium deserti sp. nov. (type strain MB418^T = CPCC 205710^T = KCTC 49782^T), and Mycobacterium hippophais sp. nov. (type strain HX176^T = CPCC 205372^T = KCTC 49413^T). Genes encoding enzymes involved in PAH degradation and metal resistance were present in the genomes of all three strains. Specifically, genes encoding alpha subunits of aromatic ring-hydroxylating dioxygenases were encoded by the genomes. The genes were also identified as core genes in a pangenomic analysis of the three strains along with 70 phylogenetically related mycobacterial strains that were previously classified as Mycolicibacterium. Notably, strain YC-RL4^T could not only utilize phthalates as their sole carbon source for growth, but also convert di-(2-ethylhexyl) phthalate into phthalic acid. These results indicated that strains YC-RL4^T, MB418^T, and HX176^T were important resources with significant bioremediation potential in soils contaminated by PAHs and heavy metals.