Bioprospecting of Soil-Derived Actinobacteria Along the Alar-Hotan Desert Highway in the Taklamakan Desert

Abstract

Taklamakan desert is known as the largest dunefield in China and as the second largest shifting sand desert in the world. Although with long history and glorious culture, the Taklamakan desert remains largely unexplored and numerous microorganisms have not been harvested in culture or taxonomically identified yet. The main objective of this study is to explore the diversity, novelty, and pharmacological potential of the cultivable actinomycetes from soil samples at various sites along the Alar-Hotan desert highway in the Taklamakan desert. A total of 590 actinobacterial strains were recovered by the culture-dependent approach. Phylogenetic analysis based on 16S ribosomal RNA (rRNA) gene sequences unveiled a significant level of actinobacterial diversity with 55 genera distributed in 27 families of 12 orders. Thirty-six strains showed relatively low 16S rRNA similarities (<98.65%) with validly described species, among which four strains had already been characterized as novel taxa by our previous research. One hundred and forty-six actinobacterial isolates were selected as representatives to evaluate the antibacterial activities and mechanism of action by the paper-disk diffusion method and a double fluorescent protein reporter “pDualrep2” system, respectively. A total of 61 isolates exhibited antagonistic activity against the tested “ESKAPE” pathogens, among which seven strains could produce bioactive metabolites either to be able to block translation machinery or to induce SOS-response in the pDualrep2 system. Notably, Saccharothrix sp. 16Sb2-4, harboring a promising antibacterial potential with the mechanism of interfering with protein translation, was analyzed in detail to gain deeper insights into its bioactive metabolites. Through ultra-performance liquid chromatography (UPLC)-quadrupole time-of-flight (QToF)-MS/MS based molecular networking analysis and databases identification, four families of compounds (1–16) were putatively identified. Subsequent bioassay-guided separation resulted in purification of four 16-membered macrolide antibiotics, aldgamycin H (8), aldgamycin K (9), aldgamycin G (10), and swalpamycin B (11), and their structures were elucidated by HR-electrospray ionization source (ESI)-MS and NMR spectroscopy. All compounds 8–11 displayed antibacterial activities by inhibiting protein synthesis in the pDualrep2 system. In conclusion, this work demonstrates that Taklamakan desert is a potentially unique reservoir of versatile actinobacteria, which can be a promising source for discovery of novel species and diverse bioactive compounds.

Diversity and bioprospecting for industrial hydrolytic enzymes of microbial communities isolated from deserted areas of south-east Morocco

“…This study revealed that Firmicutes, followed by Proteobacteria, are the most dominant phylum in Moroccan desert soils. These divisions have been observed in different hot deserts of the Tanami Desert, the Eastern Desert, and the Saudi Arabia Desert [36] , While Actinobacteria phyla was less prevalent Contrary to other studies conducted in similar locations in the Atacama Desert, Namib Desert, and Thar Desert [37] – [40] . These findings indicate that these phyla have adapted effectively to the scorching desert environment.…”

Exploring the Diversity and Antibacterial Potentiality of Cultivable Actinobacteria from the Soil of the Saxaul Forest in Southern Gobi Desert in Mongolia

“…Among these isolates, Streptomyces (20 strains), Nesterenkonia (13 strains) and Kocuria (4 strains) were the most abundant genera. Genera Streptomyces , Kocuria , Nesterenkonia , Nocardiopsis , Haloactinobacterium , Saccharopolyspora , Actinopolyspora , et al are often reported as halotolerant or halophilic actinobacteria found in salty desert environment [ 77 ]. Herein genera obtained from high-salts media agree with the previous studies on population composition of actinobacteria in different saline or hypersaline habitats.…”

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

“…Similarly, multi-membered colour-groups encompassing isolates from the northern slope of the pine forest were equated with the genera Actinacidiphila, Catenulispora, Kitasatospora, Pilimelia, Streptacidiphilus, and Streptomyces. Corresponding multi-membered colour-groups composed of isolates from the southern slope of the pine forest were either equated with the genera Actinacidiphila, Actinospica, Nocardia, and Streptomyces or were close to or bona fide members of Pilimelia columellifera subspecies pallida (Vobis et al, 1986) and Streptomyces celluloflavus (Nishimura et al, 1953) Madhaiyan et al, 2020. These data provide further evidence that 16S rRNA gene sequencing remains a practical way of determining the taxonomic status of filamentous actinomycetes isolated from extreme habitats (Goodfellow et al, 2018;Singh and Dubey, 2018;Sharma and Thakur, 2020;Liu et al, 2021).…”

“…The taxonomic data acquired in this study show that selective isolation, dereplication and initial characterization of representative isolates from diverse extreme biomes is a simple and practical way of selecting putatively novel and rare filamentous actinomycetes for exploitative biotechnology. In addition, these data underpin the rational of ecologically guided bioprospecting campaigns featuring actinomycetes (Mitra et al, 2011;Nalini and Prakash, 2017;Liu et al, 2021;Wang et al, 2022). Many of the isolates found to belong to rare and putatively novel taxa were from the litter and mineral horizons of the pine forest indicating that acidophilic and acidotolerant filamentous actinomycetes should feature more prominently in the search for novel bioactive compounds, especially given evidence that such strains are a source of novel antibiotics and acid-stable enzymes (Golińska et al, 2023).…”