Streptomyces typhae sp. nov., a novel endophytic actinomycete with antifungal activity isolated the root of cattail (Typha angustifolia L.)

A Catch-Release Strategy for the Genomics-Driven Discovery of Antiproliferative Furan-Functionalized Peptides

Furan-functionalized peptides are of significant pharmacological interest due to their pronounced bioactivities and unique potential for orthogonal bioconjugation and derivatization. However, naturally occurring peptides with furyl side chains are exceedingly rare. This study presents a streamlined method to predict and assess the microbial production of peptides incorporating 3-furylalanine (Fua) moieties. The approach integrates genome mining and the reversible, chemoselective tagging of furyl residues, utilizing their unique Diels-Alder reactivity, for mass-spectrometry-guided identification of candidate compounds. By employing the rhizonin Fua synthase as a bioinformatic handle and through heterologous reconstitution of Fua biosynthesis, we identified previously unknown Fua biosynthetic pathways in diverse bacterial phyla, including actinomycetes, cyanobacteria, actinobacteria, and γ-proteobacteria, suggesting that Fua-containing peptides are remarkably widely distributed. Metabolic profiling by reversible tagging facilitated the detection of Fua-containing metabolites in their native producers. The successful adaptation of this method for solid support enabled the direct enrichment of furyl-substituted peptides from complex mixtures. This multi-pronged approach enabled the discovery and characterization of two novel families of Fua cyclopeptides (rubriamides and typhamides) with potent antiproliferative effects against human tumor cells and nematodes. The innovative catch-and-release strategy, in conjunction with genome mining, represents a valuable tool for the discovery of new furan-substituted natural products.

Diversity and Bioactivity of Endophytic Actinobacteria Associated with the Roots of Artemisia herba-alba Asso from Algeria

The isolation of endophytic actinobacteria from the roots of wild populations of Artemisia herba-alba Asso, a medicinal plant collected from the arid lands of Algeria, is reported for the first time. Forty-five actinobacterial isolates were identified by molecular analysis and in vitro evaluated for antimicrobial activity and plant growth-promoting (PGP) abilities (1-Aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, nitrogen fixation, phosphate and potassium solubilization, ammonia, and siderophores production). The phylogenetic relationships based on 16S rRNA gene sequences show that the genus Nocardioides (n = 23) was dominant in the sampled localities. The remaining actinobacterial isolates were identified as Promicromonospora (n = 11), Streptomyces (n = 6), Micromonopora (n = 3), and Saccharothrix (n = 2). Only six (13.33%) strains (five Streptomyces and one Saccharothrix species) were antagonistic in vitro against at least one or more indicator microorganisms. The antimicrobial activity of actinobacterial strains targeted mainly Gram-positive bacteria. The results demonstrate that more than 73% of the isolated strains had ACC deaminase activity, could fix atmospheric nitrogen and were producers of ammonia and siderophores. However, only one (2.22%) strain named Saccharothrix sp. BT79 could solubilize phosphorus and potassium. Overall, many strains exhibited a broad spectrum of PGP abilities. Thus, A. herba-alba provides a source of endophytic actinobacteria that should be explored for their potential biological activities.

Enhancement of sulfur metabolism and antioxidant machinery confers Bacillus sp. Jrh14-10-induced alkaline stress tolerance in plant

Alkaline stress is a major environmental challenge that restricts plant growth and agricultural productivity worldwide. Plant growth-promoting rhizobacteria (PGPR) can be used to effectively enhance plant abiotic stress in an environment-friendly manner. However, PGPR that can enhance alkalinity tolerance are not well-studied and the mechanisms by which they exert beneficial effects remain elusive. In this study, we isolated Jrh14-10 from the rhizosphere soil of halophyte Halerpestes cymbalaria (Pursh) Green and found that it can produce indole-3-acetic acid (IAA) and siderophore. By 16S rRNA gene sequencing, it was classified as Bacillus licheniformis. Inoculation Arabidopsis seedlings with Jrh14-10 significantly increased the total fresh weight (by 148.1%), primary root elongation (by 1121.7%), and lateral root number (by 108.8%) under alkaline stress. RNA-Seq analysis showed that 3389 genes were up-regulated by inoculation under alkaline stress and they were associated with sulfur metabolism, photosynthetic system, and oxidative stress response. Significantly, the levels of Cys and GSH were increased by 144.3% and 48.7%, respectively, in the inoculation group compared to the control under alkaline stress. Furthermore, Jrh14-10 markedly enhanced the activities of antioxidant enzymes, resulting in lower levels of O2•-, H2O2, and MDA as well as higher levels of Fv/Fm in alkaline-treated seedlings. In summary, Jrh14-10 can improve alkaline stress resistance in seedlings which was accompanied by an increase in sulfur metabolism-mediated GSH synthesis and antioxidant enzyme activities. These results provide a mechanistic understanding of the interactions between a beneficial bacterial strain and plants under alkaline stress.

Streptomyces phytophilus sp. nov., an endophytic actinobacterium with biosynthesis potential as an antibiotic producer

An endophytic actinobacterium, strain PIP175^T, was isolated from the root sample of a native apricot tree (Pittosporum angustifolium) growing on the Bedford Park campus of Flinders University, Adelaide, South Australia. This strain is a Gram stain-positive, aerobic actinobacterium with well-developed substrate mycelia. Aerial mycelia rarely produce spores and the spore chain is spiral. Strain PIP175^T showed the highest 16S rRNA gene sequence similarity to Streptomyces aculeolatus DSM 41644^T (99.4 %). Other closely related phylogenetic representatives include Streptomyces synnematoformans DSM 41902^T (98.3 %), Streptomyces albospinus NBRC 13846^T (97.6 %), Streptomyces cacaoi subsp. cacaoi NRRL B-1220^T (97.5 %) and Streptomyces ruber NBRC 14600^T (97.4 %). The major cellular fatty acid of this strain was iso-C_16 : 0 and the major menaquinone was MK-9(H₆). The whole-cell sugar contained galactose, glucose and mannose. Chemotaxonomic data confirmed that strain PIP175^T belonged to the genus Streptomyces. Digital DNA-DNA hybridization, average nucleotide identity based on blast and OrthoANIu results between strain PIP175^T and S. aculeolatus DSM 41644^T were 60.0, 94.1 and 94.9 %, respectively. Genotypic and phenotypic data and genome analysis results allowed the differentiation of strain PIP175^T from its closest species with validly published names. Strain PIP175^T showed good activity against methicillin-resistant Staphylococcus aureus 03120385. Genome mining of strain PIP175^T revealed biosynthetic genes encoding proteins relating to antibiotic production, plant growth promotion and biodegradation enzymes. The name proposed for the new species is Streptomyces phytophilus sp. nov. The type strain is PIP175^T (=DSM 103379^T=TBRC 6026^T).

Streptomyces epipremni sp. nov., an endophytic actinomycete isolated from the root of Epipremnum aureum

An endophytic Streptomyces -like micro-organism, designated strain PRB2-1T was isolated from root tissue of Epipremnum aureum (Linden and André) G.S. Bunting. The typical morphological and chemotaxonomic characteristics, i.e. the ability to produce straight spore chains directly on aerial mycelium and the presence of ll-diaminopimelic acid in cell-wall peptidoglycan, were consistent with its assignment to the genus Streptomyces . 16S rRNA gene analysis showed that strain PRB2-1T is a member of the genus Streptomyces with the highest similarity to Streptomyces bryophytorum DSM 42183T (98.4 %). Moreover, the draft genome sequence of strain PRB2-1T exhibited low average nucleotide identity by blast (79.9–83.8 %) and digital DNA–DNA hybridization (24.9–28.3 %) values to the reference strains, which were well below the species circumscription threshold. The DNA G+C content of genomic DNA was 73.6 mol%. Comparison of phenotypic characteristics and whole-genome sequence between strain PRB2-1T and its close relatives indicated that strain PRB2-1T could be classified as a novel species of the genus Streptomyces . Thus the name, Streptomyces epipremni sp. nov. is proposed for the strain. The type strain is PRB2-1T (=TBRC 7642T=NBRC 113169T).

Streptomyces endocoffeicus sp. nov., an endophytic actinomycete isolated from Coffea arabica (L.)

An aerobic, non-motile, Gram-stain positive actinomycete, designated strain CA3R110^T, was isolated from the surface-sterilised root of Coffea arabica L. collected from Lampang Province, Thailand. 16S rRNA gene sequence analysis indicated that strain CA3R110^T was a member of the genus Streptomyces and showed the closest similarities to Streptomyces buecherae AC541^T (99.2%), followed by Streptomyces rapamycinicus NRRL B-5491^T (99.1%), Streptomyces luteoverticillatus NBRC 3840^T (99.1%), Streptomyces coerulescens NBRC 12758^T (99.1%), and Streptomyces iranensis HM 35^T (99.0%). Strain CA3R110^T contained LL-diaminopimelic acid in cell peptidoglycan, MK-9(H₆), and MK-9(H₈) as major menaquinone, iso-C_16:0, iso-C_15:0, C_16:0 as major fatty acids. Diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositolmannoside were detected in the cell. The chemotaxonomic characteristics possessed the typical properties of the genus Streptomyces. A low digital DNA-DNA hybridization (< 55.7%) and average nucleotide identity-blast (ANIb) (< 92.2%) values revealed that strain CA3R110^T could be distinguished from any known Streptomyces species. With the differences in phenotypic and genotypic data, strain CA3R110^T represents a novel species of genus Streptomyces, for which the name Streptomyces endocoffeicus sp. nov. is proposed. The type strain is CA3R110^T (= TBRC 11245^T = NBRC 114296^T).

Fluviispira sanaruensis sp., nov., Isolated from a Brackish Lake in Hamamatsu, Japan

Strain RF1110005^T, which was isolated from brackish lake water sampled at Lake Sanaru in Japan as a "filterable" bacterial strain, was characterized as a novel species in the genus Fluviispira, family Silvanigrellaceae, order Silvanigrellales, the class Oligoflexia and the phylum Bdellovibrionota. Cells of RF1110005^T were aerobic, Gram stain negative, and show a pleomorphic morphology of spiral, filamentous and rod shapes. Catalase reaction was positive. Strain RF1110005^T grew optimally at 30 °C, pH 7.0-8.0 and 0.5% NaCl (w/v). The major polar lipids in RF1110005^T were phosphatidylethanolamine and phosphatidylglycerol. The predominant cellular fatty acids were iso-C_15:0 and anteiso-C_15:0. Phylogenetic analysis based on 16S rRNA gene sequences and concatenates of core gene sequence showed that the nearest neighbor of strain RF1110005^T was Fluviispira multicolorata strain 33A1-SZDP^T with 98.4% 16S rRNA gene sequence similarity. The genome size of strain RF1110005^T was 3.5 Mbp with two plasmids (80 kb and 69 kb), and the G + C content was 33.7 mol%. Comparisons with genome-wide analyses and chemotaxonomic characters clearly showed that strain RF1110005^T differed from F. multicolorata. Therefore, a novel species in Fluviispira sanaruensis, sp. nov., is proposed for strain RF1110005^T (= JCM 31447 ^T = LMG 30360 ^T).