Nocardioides vastitatis sp. nov., isolated from Taklamakan desert soil

Tersicoccus mangrovi sp. nov., a novel actinobacterium from mangrove sediment in Semarang city, Indonesia

A Gram-stain-positive, aerobic and non-motile actinobacterium, designated strain MR15.9T, was isolated from sediment collected from a mangrove ecosystem in Semarang city, Indonesia. Strain MR15.9T grew at 4-37 °C (optimum 30 °C), pH 6.0-11.0 (optimum 7.0-8.0), with 0-10% (w/v) NaCl (optimum 0-3%). The genome of strain MR15.9T was 3.67 Mbp with 71.7 mol% G+C content. Phylogenetic analysis based on 16S rRNA gene sequence and genome sequence directed that strain MR15.9T formed a well-supported clade with Tersicoccus solisilvae CGMCC 1.15480T and Tersicoccus phoenicis 1P05MAT and shared the highest similarity to T. solisilvae CGMCC 1.15480T (98.9% sequence similarity) and T. phoenicis 1P05MAT (98.6% sequence similarity). However, the comparative genome analysis between strain MR15.9T and T. solisilvae CGMCC 1.15480T gave average nt identity value of 85.2% and digital DNA-DNA hybridization value of 29.0%, which were below the statistical threshold for the delineation of the species. Chemotaxonomic data showed that the major fatty acids were anteiso-C15:0, anteiso-C17:0 and iso-C16:0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unidentified glycolipids and two unidentified phospholipids. MK-8(H2) and MK-9(H2) were noted as the predominant respiratory quinones in this strain. The results of polyphasic characterization indicated that strain MR15.9T represents a novel species of the genus Tersicoccus. The name Tersicoccus mangrovi sp. nov. is proposed, with the type strain MR15.9T (=MCCC 1K08875T=KCTC 59105T).

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).

Nocardioides jiangxiensis sp. nov., a novel actinobacterium isolated from lakeside soil, exhibiting the biosynthesis potential of mycofactocin

A Gram-stain-positive, rod-shaped, non-spore-forming and non-motile bacterium, designated WY-20T, was isolated from a lakeside soil sample collected in Jiangxi Province, PR China. Growth was observed at 20-42 °C (optimum 30 °C), pH 5.0-8.0 (optimum pH 7.0) and salinity of 0-3.0% (w/v; optimum 0.5%). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain WY-20T belongs to the genus Nocardioides and showed the highest sequence similarity (98.1%) to N. phosphati WYH11-7T, followed by N. cavernaquae K1W22B-1T (97.8%), N. marmoriterrae JOS5-1T (97.2%) and N. jensenii NBRC 14755T (97.1%). The average nucleotide identity and digital DNA-DNA hybridization values between strains WY-20T and N. phosphati WYH11-7T were 83.5% and 26.2%, respectively. The predominant fatty acids (≥ 10% of the total fatty acids) were C18:1ω9c, C17:0, C16:0, summed feature 8 (C18:1ω7c and/or C18: 1ω6c) and C17:1ω9c. The major menaquinone was MK-8 (H4). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unidentified phospholipids. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. Based on phenotypic, genotypic and phylogenetic pieces of evidence, strain WY-20T represents a novel species in the genus Nocardioides, for which the name Nocardioides jiangxiensis sp. nov. is proposed. The type strain is WY-20T (= GDMCC 4.317T = KACC 23379T).

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.

Description of Nocardioides piscis sp. nov., Sphingomonas piscis sp. nov. and Sphingomonas sinipercae sp. nov., isolated from the intestine of fish species Odontobutis interrupta (Korean spotted sleeper) and Siniperca scherzeri (leopard mandarin fish)

A polyphasic taxonomic approach was used to characterize three novel bacterial strains, designated as HDW12AT, HDW-15BT, and HDW15CT, isolated from the intestine of fish species Odontobutis interrupta or Siniperca scherzeri. All isolates were obligate aerobic, non-motile bacteria, and grew optimally at 30°C. Phylogenetic analysis based on 16S rRNA sequences revealed that strain HDW12AT was a member of the genus Nocardioides, and closely related to Nocardioides allogilvus CFH 30205T (98.9% sequence identities). Furthermore, strains HDW15BT and HDW15CT were members of the genus Sphingomonas, and closely related to Sphingomonas lutea JS5T and Sphingomonas sediminicola Dae 20T (97.1% and 97.9% sequence identities), respectively. Strain HDW12AT contained MK-8 (H4), and strains HDW15BT and HDW15CT contained Q-10 as the respiratory quinone. Major polar lipid components of strain HDW12AT were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylinositol, and those of strains HDW15BT and HDW15CT were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The G + C content of strains HDW12AT, HDW15BT, and HDW15CT were 69.7, 63.3, and 65.5%, respectively. The results of phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses suggest that strain HDW12AT represents a novel species within the genus Nocardioides, and strains HDW15BT and HDW15CT represent two novel species within the genus Sphingomonas. We propose the names Nocardioides piscis for strain HDW12AT (= KACC 21336T = KCTC 49321T = JCM 33670T), Sphingomonas piscis for strain HDW15BT (= KACC 21341T = KCTC 72588T = JCM 33738T), and Sphingomonas sinipercae for strain HDW15CT (= KACC 21342T = KCTC 72589T = JCM 33739T).

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

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.