Kitasatospora fiedleri sp. nov., a novel antibiotic-producing member of the genus Kitasatospora

Application of a replicative targetable vector system for difficult-to-manipulate streptomycetes

The low frequency of homologous recombination together with poor efficiency in introducing DNA into the cell are the main factors hampering genetic manipulation of some bacterial strains. We faced this problem when trying to construct mutants of Streptomyces iranensis DSM 41954, a strain in which conjugation is particularly inefficient, and suicidal vectors had failed to yield any exconjugants. In this work, we report the construction and application of a conjugative replicative vector, pDS0007, which allows selection of exconjugants even with poor conjugation efficiency. The persistence of the construct inside the cell for as long as required facilitates the homologous recombination events leading to single and double crossovers. While it was confirmed that the vector is frequently lost without selection, the recognition sequence for the I-SceI endonuclease was included in the backbone of pDS0007. The presence of a I-SceI recognition sequence would allow to force the loss of the vector and the appearance of double crossover recombinants by introducing a second construct (e.g. pIJ12742) that expresses a Streptomyces codon-optimised gene encoding the I-SceI endonuclease. To facilitate screening for vector-free clones, the construct also carries a Streptomyces codon-optimised gusA gene encoding the β-glucuronidase expressed from a constitutive promoter. We prove the usefulness of this vector and strategy with the strain S. iranensis DSM 41954, in which we could readily delete an essential gene of a newly discovered biosynthetic pathway for a phosphonate-containing natural product, which led to loss of phosphonate production according to 31P NMR spectroscopy. KEY POINTS: • pDS0007 is a new vector for gene-targeting in difficult-to-manipulate streptomycetes. • pDS0007 is self-replicative but easy to cure, targetable and allows visual screening. • pDS0007 was used to prove the discovery of a novel phosphonate biosynthetic pathway.

The effects of livestock grazing on physicochemical properties and bacterial communities of perlite-rich soil

Livestock grazing has been proposed as a cost-effective way to reclaim post-mining lands. It can enhance soil fertility and biodiversity, but its impacts on soil quality and microbial communities vary across soil types. Moreover, waste from grazing raises concerns about pathogens that could pose risks to animal and human health. This study investigated the effects of grazing on post-mining perlite-rich soil in central Thailand. A comparative analysis of soil physicochemical properties and bacterial diversity was conducted between grazed and ungrazed sites. Bacterial diversity was assessed using 16S amplicon sequencing. The perlite-rich soil was found to be sandy, acidic, and to have low nutritional content. Grazing significantly improved the soil texture and nutrient content, suggesting its potential as a cost-effective reclamation strategy. The 16S metagenomic sequencing analysis revealed that microbial communities were impacted by livestock grazing. Specifically, shifts in the dominant bacterial phyla were identified, with increases in Firmicutes and Chloroflexi and a decrease in Actinobacteria. Concerns about increased levels of pathogenic Enterobacteriaceae due to grazing were not substantiated in perlite-rich soil. These bacteria were consistently found at low levels in all soil samples, regardless of livestock grazing. This study also identified a diverse population of Streptomycetaceae, including previously uncharacterized strains/species. This finding could be valuable given that this bacterial family is known for producing antibiotics and other secondary metabolites. However, grazing adversely impacted the abundance and diversity of Streptomycetaceae in this specific soil type. In line with previous research, this study demonstrated that the response of soil microbial communities to grazing varies significantly depending on the soil type, with unique responses appearing to be associated with perlite-rich soil. This emphasizes the importance of soil-specific research in understanding how grazing affects microbial communities. Future research should focus on optimizing grazing practices for perlite-rich soil and characterizing the Streptomycetaceae community for potential antibiotic and secondary metabolite discovery. The obtained findings should ultimately contribute to sustainable post-mining reclamation through livestock grazing and the preservation of valuable microbial resources.

Challenging old microbiological treasures for natural compound biosynthesis capacity

Strain collections are a treasure chest of numerous valuable and taxonomically validated bioresources. The Leibniz Institute DSMZ is one of the largest and most diverse microbial strain collections worldwide, with a long tradition of actinomycetes research. Actinomycetes, especially the genus Streptomyces, are renowned as prolific producers of antibiotics and many other bioactive natural products. In light of this, five Streptomyces strains, DSM 40971T, DSM 40484T, DSM 40713T, DSM 40976T, and DSM 40907T, which had been deposited a long time ago without comprehensive characterization, were the subject of polyphasic taxonomic studies and genome mining for natural compounds based on in vitro and in silico analyses. Phenotypic, genetic, and phylogenomic studies distinguished the strains from their closely related neighbors. The digital DNA-DNA hybridization and average nucleotide identity values between the five strains and their close, validly named species were below the threshold of 70% and 95%-96%, respectively, determined for prokaryotic species demarcation. Therefore, the five strains merit being considered as novel Streptomyces species, for which the names Streptomyces kutzneri sp. nov., Streptomyces stackebrandtii sp. nov., Streptomyces zähneri sp. nov., Streptomyces winkii sp. nov., and Streptomyces kroppenstedtii sp. nov. are proposed. Bioinformatics analysis of the genome sequences of the five strains revealed their genetic potential for the production of secondary metabolites, which helped identify the natural compounds cinerubin B from strain DSM 40484T and the phosphonate antibiotic phosphonoalamide from strain DSM 40907T and highlighted strain DSM 40976T as a candidate for regulator-guided gene cluster activation due to the abundance of numerous "Streptomyces antibiotic regulatory protein" (SARP) genes.