Streptomyces alkaliphilus sp. nov., isolated from sediments of Lake Elmenteita in the Kenyan Rift Valley

Molecular characterization and phylogenetic diversity of actinomycetota species isolated from Lake Natron sediments at Arusha, Tanzania

Soda lakes are naturally occurring ecosystems characterized by extreme environmental conditions especially high pH and salinity levels but harboring valuable microbial communities with medical and biotechnological potentials. Lake Natron is one of the soda lakes situated in eastern branch of the East African Gregory Rift valley, Tanzania. In this study, the taxonomy and phylogenetic diversity of Actinomycetota species were explored in Lake Natron using molecular techniques. The sequencing of their 16S rRNA gene resulted into 13 genera of phylum Actinomycetota namely Streptomyces, Microbacterium, Nocardiopsis, Gordonia, Dietzia, Micromonospora, Microcella, Pseudarthrobacter, Nocardioides, Actinotalea, Cellulomonas, Isoptericola, and Glutamicibacter. We describe for the first time, the isolation of Streptomyces lasalocidi, S. harbinensis, S. anthocyanicus, Microbacterium aureliae, Pseudarthrobacter sp., Nocardioides sp. and Glutamicibacter mishrai from soda lake habitats. It also reports for the first time, the isolation of Gordonia spp., Microcella sp. and Actinotalea sp. from an East African Soda Lake as well as isolation of S. pseudogriseolus, S. calidiresistens and Micromonospora spp. from a Tanzania soda lake. Furthermore, two putative novel species of the phylum Actinomycetota were identified. Given that Actinomycetota are known potential sources of important biotechnological compounds, we recommend the broadening of the scope of bioprospection in future to include the novel species from Lake Natron.

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.

Streptomyces alkaliterrae sp. nov., isolated from an alkaline soil, and emended descriptions of Streptomyces alkaliphilus, Streptomyces calidiresistens and Streptomyces durbertensis

A polyphasic study was undertaken to establish the taxonomic position of six representative streptomycetes isolated from an alkaline soil adjacent to a meteoric alkaline soda lake in India. Chemotaxonomic, cultural and morphological properties of the isolates were consistent with their classification in the genus Streptomyces. The isolates formed extensively branched substrate mycelia and aerial hyphae that differentiated in straight chains of spores with smooth surfaces. They contained LL-diaminopimelic acid in the wall peptidoglycan, produced either hexa- or octa-hydrogenated menaquinones with nine isoprene units, major amounts of saturated, iso- and anteiso- fatty acids and phosphatidylethanolamine as the characteristic polar lipid. The isolates grew well at 30 °C, pH 9 and in the presence of 3 to 5% (w/v) sodium chloride. Isolates OF1^T, OF3 and OF8 formed a distinct clade within the Streptomyces 16S rRNA gene tree sharing relatively high sequence similarities with the type strains of Streptomyces durbertensis (99.3%), Streptomyces palmae (98.1%) and Streptomyces xinghaiensis (98.3%), but can be distinguished from them using combinations of phenotypic properties. A phylogenomic tree based on draft genome sequences of the isolates and S. durbertensis DSM 104538^T confirmed the phylogenetic relationships. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values calculated from the whole genome sequences of isolate OF1^T and S. durbertensis DSM 104538^T were low at 92.0% and 45.2%, respectively, indicating that they belong to different genomic species. Consequently, on the basis of the genomic, phylogenetic and associated phenotypic data it is proposed that isolates OF1^T, OF3 and OF8 be assigned to the genus Streptomyces as Streptomyces alkaliterrae sp. nov. with strain OF1^T (NCIMB 15195^T =PCM 3001^T) as the type strain. Isolates IF11, IF17 and IF19, and S. alkaliphilus DSM 42118^T were shown to belong to the same taxospecies and together with S. calidiresistens DSM 42108^T comprised a well supported clade in the Streptomyces 16S rRNA gene tree. Isolate IF17 and S. alkaliphilus DSM 42118^T formed a well-supported clade in the phylogenomic tree, had almost identical digital G + C similarity values, produced long straight chains of smooth-surfaced spores and shared ANI and dDDH values (98.0 and 79.6%, respectively) consistent with their assignment to the same genomic species. In light of all of the data isolates IF11, IF17 and IF19 should be seen as authentic stains of S. alkalihilus. Data acquired in the present study have also been used to emend the descriptions of S. alkaliphilus, S. calidiresistens and S. durbertensis. The genomes of isolates IF17, and OF1^T, OF3 and OF8 contain relatively high numbers of biosynthetic gene clusters some of which were discontinously distributed indicating ones predicted to express for novel specialised metabolites.

Streptomyces sediminis sp. nov. isolated from crater lake sediment

A novel actinobacterial strain, MKSP12^T, was isolated from coastal sediment of a crater lake in central Anatolia, Turkey. The taxonomic position of the strain was clarified using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain MKSP12^T is closely related to Streptomyces specialis GW 41-1564^T with 97.1% sequence similarity. The strain produces aerial hyphae that differentiate into spiral chains of smooth surfaced spores and grows over a temperature range of 20-37 °C, at pH 7-11 and in the presence of 3% (w/v) sodium chloride. The cell wall amino acid is LL-diaminopimelic acid and the whole cell sugars are glucose and ribose. The polar lipids profile consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified aminophospholipid, two unidentified phospholipids, an unidentified glycophospholipid and eight unidentified glycolipids; iso-C_16:0, iso-C_16:1 G, anteiso-C_17:0 and anteiso-C_17:1 ω9c were identified as the predominant cellular fatty acids (> 10%). Based on morphological and chemotaxonomic characteristics, and phylogenetic analyses, the strain is considered to represent a novel species in the genus Streptomyces, for which the name Streptomyces sediminis sp. nov. is proposed with the type strain MKSP12^T (= DSM 100692^T = KCTC 39613^T).

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. Note that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.