Streptomyces: Still the Biggest Producer of New Natural Secondary Metabolites, a Current Perspective

There is a real consensus that new antibiotics are urgently needed and are the best chance for combating antibiotic resistance. The phylum Actinobacteria is one of the main producers of new antibiotics, with a recent paradigm shift whereby rare actinomycetes have been increasingly targeted as a source of new secondary metabolites for the discovery of new antibiotics. However, this review shows that the genus Streptomyces is still the largest current producer of new and innovative secondary metabolites. Between January 2015 and December 2020, a significantly high number of novel Streptomyces spp. have been isolated from different environments, including extreme environments, symbionts, terrestrial soils, sediments and also from marine environments, mainly from marine invertebrates and marine sediments. This review highlights 135 new species of Streptomyces during this 6-year period with 108 new species of Streptomyces from the terrestrial environment and 27 new species from marine sources. A brief summary of the different pre-treatment methods used for the successful isolation of some of the new species of Streptomyces is also discussed, as well as the biological activities of the isolated secondary metabolites. A total of 279 new secondary metabolites have been recorded from 121 species of Streptomyces which exhibit diverse biological activity. The greatest number of new secondary metabolites originated from the terrestrial-sourced Streptomyces spp.

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.

Resistance and resilience of soil prokaryotic communities in response to prolonged drought in a tropical forest

Global climate changes such as prolonged duration and intensity of drought can lead to adverse ecological consequences in forests. Currently little is known about soil microbial community responses to such drought regimes in tropical forests. In this study, we examined the resistance and resilience of topsoil prokaryotic communities to a prolongation of the dry season in terms of diversity, community structure and co-occurrence patterns in a French Guianan tropical forest. Through excluding rainfall during and after the dry season, a simulated prolongation of the dry season by five months was compared to controls. Our results show that prokaryotic communities increasingly diverged from controls with the progression of rain exclusion. Furthermore, prolonged drought significantly affected microbial co-occurrence networks. However, both the composition and co-occurrence networks of soil prokaryotic communities immediately ceased to differ from controls when precipitation throughfall returned. This study thus suggests modest resistance but high resilience of microbial communities to a prolonged drought in tropical rainforest soils.

Streptomyces apocyni sp. nov., an endogenous actinomycete isolated from Apocynum venetum

A novel actinomycete, designated strain TRM 66233^T, was isolated from Apocynum venetum L. collected from the Xinjiang Uygur Autonomous Region of China and characterized using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain TRM 66233^T with the genus Streptomyces. Strain TRM 66233^T showed a high similarity value to Streptomyces bikiniensis NRRL B-1049^T (98.07 %) based on the 16S rRNA gene phylogenetic tree. The whole-cell sugar pattern of TRM 66233^T consisted of glucose, galactose, mannose and ribose. The predominant menaquinones were MK-9(H₂), MK-9(H₆), MK-9(H₈) and MK-9(H₁₀). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and four unidentified lipids. The major fatty acids were iso-C_15 : 0, anteiso-C_15 : 0, iso-C_16 : 0, C_16 : 0 and iso-C_17 : 0. The G+C content of the DNA was 70.35 mol%. The DNA-DNA relatedness and average nucleotide identity values as well as evolutionary distances based on multilocus (atpD, gyrB, recA, rpoB and trpB) sequences between strain TRM 66233^T and closely related type strains were significantly lower than the recommended threshold values. The whole-genome average nucleotide identity and digital DNA-DNA hybridization values between strain TRM 66233^T and S. bikiniensis NRRL B-1049^T were 78.86 and 23.2 %, respectively. On the basis of evidence from this polyphasic study, strain TRM 66233^T should represent a novel species of the genus Streptomyces, for which the name Streptomyces apocyni sp. nov. is proposed. The type strain is TRM 66233^T (=CCTCC AA 2019056^T=LMG 31559^T).

Streptomyces tibetensis sp. nov., an actinomycete isolated from the Tibetan Plateau

A novel actinomycete, designated strain XZ 46^T, was isolated from acid sandy soil collected from the Tibetan Plateau, China. Its taxonomic position was determined using a polyphasic approach. Strain XZ 46^T shows the typical morphological and chemotaxonomic features of members of the genus Streptomyces: slightly yellow to brown substrate mycelia and grayish white to slightly yellow aerial hyphae forming cylindrical and spiny spores; meso-diaminopimelic acid in the cell wall peptidoglycan; MK-9(H₈), MK-9(H₄) and MK-9(H₂) as predominant menaquinones; diphosphatidylglycerol, phospatidylethanolamine, phosphatidylglycerol and phosphatidylinositol as main polar lipids; and iso-C_15:0, iso-C_16:0 and anteiso-C_15:0 as major cellular fatty acids. The G+C content of the draft genome sequence, consisting of 8,995,813 bp, is 71.23%. The16S rRNA gene sequence analysis indicated that strain XZ 46^T shows high sequence similarity to Streptomyces luteogriseus NBRC 13402^T as well as forming an independent lineage clade with it in phylogenetic trees. Multilocus sequence analysis (MLSA) of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) illustrated that Streptomyces hawaiiensis is also a very closely related taxon. However, DNA-DNA hybridization, MLSA evolutionary distance and phenotypic properties demonstrate that strain XZ 46^T can be distinguished from these phylogenetically related Streptomyces species. Therefore, it is concluded that strain XZ 46^T represents a novel species of the genus Streptomyces, for which the name Streptomyces tibetensis is sp. nov. proposed. The type strain is XZ 46^T (= CGMCC 4.7579^T = KCTC 49221^T).