Labedella phragmitis sp. nov. and Labedella populi sp. nov., two endophytic actinobacteria isolated from plants in the Taklamakan Desert and emended description of the genus Labedella

Phycicoccus sonneraticus sp. nov., a Novel Endophytic Actinobacterium Isolated from the Bark of Sonneratia apetala

A novel endophytic actinobacterial strain, designated MQZ13P-5T, was isolated from a piece of bark of Sonneratia apetala, collected from Guangxi Zhuang Autonomous Region, China. This strain was Gram-stain positive, aerobic, non-spore-forming, non-motile and rod-shaped. Comparative 16S rRNA gene sequence analysis showed that strain MQZ13P-5T was related to the genus Phycicoccus with exhibiting the highest similarity (98.0%) to Phycicoccus endophyticus IP6SC6T. The phylogenetic trees based on 16S rRNA gene sequences and core genes indicated that strain MQZ13P-5T belonged to the genus Phycicoccus and could not be assigned to any described species. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MQZ13P-5T and type strains of Phycicoccus species were less than 84% and 27%, respectively, below the thresholds for species delineation. This strain showed chemotaxonomic and phenotypic properties consistent with its classification in the genus Phycicoccus. Based on the taxonomic data, strain MQZ13P-5T should represent a novel species of the genus Phycicoccus, for which the name Phycicoccus sonneraticus sp. nov. is proposed, with the type strain MQZ13P-5T (= CGMCC 1.18744T = JCM 34337T).

Protaetiibacter mangrovi sp. nov., isolated from mangrove soil

A novel Gram-stain-positive, aerobic, non-flagellated and rod-shaped actinobacterium, designated 10F1B-8-1T, was isolated from mangrove soil sampled at Futian Mangrove Nature Reserve, China. The isolate was able to grow at 10-40 °C (optimum 30-32 °C), at pH 6-8 (optimum 7) and in the presence of 0-6% (w/v) NaCl (optimum 0%). Strain 10F1B-8-1T shared the highest 16S rRNA gene sequence similarity to Protaetiibacter larvae NBRC 113051T (98.3%), followed by Protaetiibacter intestinalis NBRC 113050T (98.2%). Phylogenetic trees based on 16S rRNA gene sequences and the core proteomes exhibited that strain 10F1B-8-1T formed a new phyletic line in the clade of genus Protaetiibacter, indicating that this strain belonged to the genus Protaetiibacter. Strain 10F1B-8-1T showed low average nucleotide identity (<84%) and digital DNA-DNA hybridization values (<27%) with closely related taxa, suggesting that strain 10F1B-8-1T was a hitherto undescribed species of the genus Protaetiibacter. Strain 10F1B-8-1T contained D-2,4-diaminobutyric acid as the diagnostic diamino acid, and the peptidoglycan type was characterized as type B2β. The major fatty acids were iso-C16:0, anteiso-C15:0 and anteiso-C17:0. The major menaquinones were MK-13 and MK-14. The polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid and five unidentified lipids. Notably, the ethyl acetate extracts of strain 10F1B-8-1T showed effective antibacterial activity against Bacillus subtilis CPCC 100029 and Escherichia coli △tolC. According to the polyphasic data, strain 10F1B-8-1T should be classified as a novel species of the genus Protaetiibacter, for which the name Protaetiibacter mangrovi sp. nov. is proposed, with the type strain 10F1B-8-1T (=JCM 33142T = CPCC 205428T).

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.

Schumannella soli sp. nov., a novel actinomycete isolated from mangrove soil by in situ cultivation

A novel actinobacterial strain, designated 10F1D-1^T, was isolated from soil sample collected from Futian mangrove nature reserve, China using of the in situ cultivation technique. Preliminary analysis based on the 16S rRNA gene sequence revealed that strain 10F1D-1^T was the member of genus Schumannella with sharing highest sequence similarity (99.7%) to Schumannella luteola DSM 23141^T. Phylogenetic analyses based on 16S rRNA gene sequences and core proteome consistently exhibited that strain 10F1D-1^T formed a monophyletic clade with Schumannella luteola DSM 23141^T. Comparative genomic analyses clearly separated strain 10F1D-1^T from the only species of the genus Schumannella based on average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values below the thresholds for species delineation. The genome of strain 10F1D-1^T contains the biosynthetic gene clusters for osmoprotectants to adapt to the salt environment of mangrove. Strain 10F1D-1^T also contains the biosynthetic gene clusters for bioactive compounds as secondary metabolites. On the basis of the polyphasic analysis, strain 10F1D-1^T is considered to represent a novel species of the genus Schumannella, for which the name Schumannella soli sp. nov. (type strain 10F1D-1^T = CGMCC1.16699^T = JCM 33146^T) is proposed.

Diversity, novelty, antimicrobial activity, and new antibiotics of cultivable endophytic actinobacteria isolated from psammophytes collected from Taklamakan Desert

Three hundred and twenty endophytic actinobacterial strains were isolated from psammophytes collected from Taklamakan Desert and identified. Among them, three strains already had been identified as new species of two genera and sixteen isolates showed relatively low 16S rRNA similarities < 98.6% to validly described species. Seventy-five of the isolates were selected as representative strains to screen antibacterial activity and mechanism. Forty-seven strains showed antagonistic activity against at least one of the indicator bacteria. Two Streptomyces strains produced bioactive compounds inducing DNA damage, and two Streptomyces strains produced bioactive compounds with inhibitory activity on protein biosynthesis. Notably, the strain Streptomyces sp. 8P21H-1 that demonstrated both strong antibacterial activity and inhibitory activity on protein biosynthesis was prioritized for exploring new antibiotics. Under the strategy of integrating genetics-based discovery program and MS/MS-based molecular networking, two new streptogramin-type antibiotics, i.e., acetyl-griseoviridin and desulphurizing griseoviridin, along with known griseoviridin, were isolated from the culture broth of strain 8P21H-1. Their chemical structures were determined by HR-MS, and 1D and 2D NMR. Desulphurizing griseoviridin and griseoviridin exhibited antibacterial activities by inhibiting translation.

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.

Actinobacteria Associated with Vineyard Soils of Algeria: Classification, Antifungal Potential Against Grapevine Trunk Pathogens and Plant Growth-Promoting Features

Grapevine trunk diseases (GTDs) are among the most destructive diseases of vineyards worldwide, including Algeria. In the fungal complex involved in GTD symptoms, referred as grapevine trunk-pathogens, Paeomoniella chlamydospora and Phaeoacremonium minimum have a determining infecting role as pioneer fungi. Due to the lack of efficiency of conventional disease management practices, a search for alternative strategies, such as biocontrol, is needed. Taking the approach of looking for biocontrol candidates in the environment surrounding the plant, the present study explored actinobacteria diversity within vineyard soils of six grape-producing regions in Algeria. Based on their 16S rRNA gene sequence, identification and phylogenic analysis were performed on the 40 isolates of actinobacteria obtained. Forty percent of strains were attached to Streptomyces, including two evidenced new species, and 32.5% were affiliated to Saccharothrix. The other less represented genera were Actinoplanes, Nocardia, Nocardiopsis, Lentzea, Nonomuraea, Promicromonospora, Saccharopolyspora and Streptosporangium. Screening based on antagonistic and plant growth promotion (PGP) abilities of the strains showed that 47.5% of the isolates exhibited appreciable antagonistic activities against both Pa. chlamydospora and Pm. minimum, with the two best strains being Streptomyces sp. Ms18 and Streptomyces sp. Sb11. Screening for plant growth promoting properties demonstrated that majority of the strains were able to produce indole acetic acid, siderophores, ammonia, ACC deaminase, cellulase and amylase, and fix N₂. Through a PGP-traits-based cluster analysis, the most interesting strains were highlighted. Taking into account both antagonistic and PGP properties, Streptomyces sp Sb11 was selected as the most promising candidate for further evaluations of its efficiency in a GTDs context.