Genome sequence of Umezawaea sp. strain Da 62-37 isolated from the rhizosphere of Deschampsia antarctica E.Desv. (Galindez Island, maritime Antarctic).

In this study, we present the genome sequence of Umezawaea sp. strain Da 62-37, which was isolated from the rhizosphere of Deschampsia antarctica E.Desv. (Galindez Island, maritime Antarctic). The de novo assembly produced one contig, with a length of 11,793,683 bp. AntiSMASH analysis indicated 49 biosynthetic gene clusters.

Bacterial community and culturable actinomycetes of Phyllostachys viridiglaucescens rhizosphere.

During the course of development plants form tight interactions with microorganisms inhabiting their root zone. In turn, rhizosphere bacteria, in particular members of the phylum Actinomycetota, positively influence the host plant by increasing access to essential nutrients and controlling the pathogenic microorganism's population. Herein, we report the characterisation of the rhizosphere associated actinobacteria community of Phyllostachys viridiglaucescens growing in the Nikitsky Botanical Garden (Crimean Peninsula, Ukraine). The overall composition of the bacterial community was elucidated by 16S rRNA gene amplicon sequencing followed by isolation of culturable microorganisms with the focus on actinomycetes. The metagenomic approach revealed that the representatives of phylum Actinomycetota (57.1%), Pseudomonadota (20.0%), and Acidobacteriota (12.2%) were dominating in the studied microbiome with Ilumatobacter (phylum Actinomycetota) (13.1%) being the dominant genus. Furthermore, a total of 159 actinomycete isolates, belonging to eight genera of Streptomyces, Micromonospora, Nonomuraea, Arthrobacter, Actinomadura, Kribbella, Cellulosimicrobium, and Mumia, were recovered from P. viridiglaucescens rhizosphere. The isolated species were tested for antimicrobial activity. 64% of isolates were active against at least one bacterial test-culture and 7.5% against fungal test culture. In overall, the rhizosphere bacterial communities act as a great source of actinobacterial diversity with the high potential for production of new bioactive compounds.

Draft genome sequence of Enterococcus sp. SB12 isolated from artisanal cheese of the Carpathian.

In this study, we present the draft genome sequence of the Enterococcus sp. strain SB12, which was isolated from artisanal cheese of the Carpathian region (Ukraine). The de novo assembly produced 64 contigs, with a total length of 2,514,601 bp. Phylogenetic analysis revealed its proximity to the Enterococcus faecium strains.

Diversity and bioactive potential of Actinomycetia from the rhizosphere soil of Juniperus excelsa.

Microbial natural products are among the main sources of compounds used in the medical biotechnology field for the purpose of drug development. However, as antibiotic resistance in pathogenic microorganisms is known to be increasing dramatically, there exists a need to develop new antibiotics. Actinomycetia have proven to be a good source of biologically active compounds, although the rediscovery of previously known compounds significantly slows down the introduction of new antibiotics. As a consequence, increasing attention is being paid to the isolation of actinomycete strains from previously unexplored sources, which can significantly increase the likelihood of discovering new biologically active compounds. This study investigated the diversity and bioactive potential of 372 actinomycete strains isolated from the rhizosphere soil of Juniperus excelsa M. Bieb. The examined actinomycete strains belonged to 11 genera, namely, Actinoplanes, Actinorectispora, Amycolatopsis, Kribbella, Micrococcus, Micromonospora, Nocardia, Promicromonospora, Rhodococcus, Saccharopolyspora and Streptomyces. The bioactive potential of each isolated actinomycete strain was determined on the basis of its ability to produce antimicrobial metabolites against Gram-positive and Gram-negative bacteria and yeast. Some 159 strains (42.74%) exhibited antimicrobial activity against at least one of the tested microbial strains. The dereplication analysis of the extract of the Streptomyces sp. Je 1-651 strain, which exhibited strong antimicrobial activity, led to the annotation of spiramycins and stambomycins. Moreover, the phylogenetic analysis based on the 16S rRNA gene sequence of the Je 1-651 strain revealed it to be close to the S. ambofaciens.

Flavacol and Its Novel Derivative 3-ß-Hydroxy Flavacol from Streptomyces sp. Pv 4-95 after the Expression of Heterologous AdpA.

Actinomycetes are one of the main producers of biologically active compounds. However, their capabilities have not been fully evaluated due to the presence of many unexpressed silent clusters; moreover, actinomycetes can probably produce new or previously discovered natural products under certain conditions. Overexpressing the adpA gene into streptomycetes strains can unlock silent biosynthetic gene clusters. Herein, we showed that by applying this approach to Streptomyces sp. Pv 4-95 isolated from Phyllostachys viridiglaucescens rhizosphere soil, two new mass peaks were identified. NMR structure analysis identified these compounds as flavacol and a new 3-ß-hydroxy flavacol derivative. We suggest that the presence of heterologous AdpA has no direct effect on the synthesis of flavacol and its derivatives in the Pv 4-95 strain. However, AdpA affects the synthesis of precursors by increasing their quantity, which then condenses into the resulting compounds.

Furaquinocins K and L: Novel Naphthoquinone-Based Meroterpenoids from Streptomyces sp. Je 1-369.

Actinomycetes are the most prominent group of microorganisms that produce biologically active compounds. Among them, special attention is focused on bacteria in the genus Streptomyces. Streptomycetes are an important source of biologically active natural compounds that could be considered therapeutic agents. In this study, we described the identification, purification, and structure elucidation of two new naphthoquinone-based meroterpenoids, furaquinocins K and L, from Streptomyces sp. Je 1-369 strain, which was isolated from the rhizosphere soil of Juniperus excelsa (Bieb.). The main difference between furaquinocins K and L and the described furaquinocins was a modification in the polyketide naphthoquinone skeleton. In addition, the structure of furaquinocin L contained an acetylhydrazone fragment, which is quite rare for natural compounds. We also identified a furaquinocin biosynthetic gene cluster in the Je 1-369 strain, which showed similarity (60%) with the furaquinocin B biosynthetic gene cluster from Streptomyces sp. KO-3988. Furaquinocin L showed activity against Gram-positive bacteria without cytotoxic effects.

Screening of Thiopeptide-Producing Streptomycetes Isolated From the Rhizosphere Soil of Juniperus excelsa.

The identification of an increasing number of drug-resistant pathogens has stimulated the development of new therapeutic agents to combat them. Microbial natural products are among the most important elements when it comes to drug discovery. Today, thiopeptide antibiotics are receiving increasing research attention due to their potent activity against Gram-positive bacteria. In this study, we demonstrated the successful use of a whole-cell microbial biosensor (Streptomyces lividans TK24 pMO16) for the specific detection of thiopeptide antibiotics among the native actinomycete strains isolated from the rhizosphere soil of Juniperus excelsa (Bieb.). Among the native strains, two strains of Streptomyces, namely sp. Je 1-79 and Je 1-613, were identified that were capable of producing thiopeptide antibiotics. A multilocus sequence analysis of five housekeeping genes (gyrB, atpD, recA, rpoB, and trpB) classified them as representatives of two different species of the genus Streptomyces. The thiopeptide antibiotics berninamycin A and B were identified in the extracts of the two strains by means of a dereplication analysis. The berninamycin biosynthetic gene cluster was also detected in the genome of the Streptomyces sp. Je 1-79 strain and showed a high level of similarity (93%) with the ber cluster from S. bernensis. Thus, the use of this whole-cell biosensor during the first stage of the screening process could serve to accelerate the specific detection of thiopeptide antibiotics.

Design, development and application of whole-cell based antibiotic-specific biosensor.

Synthetic biology techniques hold great promise for optimising the production of natural products by microorganisms. However, evaluating the phenotype of a modified bacterium represents a major bottleneck to the engineering cycle - particularly for antibiotic-producing actinobacteria strains, which grow slowly and are challenging to genetically manipulate. Here, we report the generation and application of antibiotic-specific whole-cell biosensor derived from TetR transcriptional repressor for use in identifying and optimising antibiotic producers. The constructed biosensor was successfully used to improve production of polyketide antibiotic pamamycin. However, an initial biosensor based on native genetic elements had inadequate dynamic and operating ranges. To overcome these limitations, we fine-tuned biosensor performance through alterations of the promoter and operator of output module and the ligand affinity of transcription factor module, which enabled us to deduce recommendations for building and application of actinobacterial biosensors.

The adpA-like regulatory gene from Actinoplanes teichomyceticus: in silico analysis and heterologous expression.

Analysis of the draft sequence of the genome of teicoplanin producer Actinoplanes teichomyceticus (NRRL-B16726) led to identification of several genes encoding AraC-family regulators that resemble AdpA, master regulator of transcription in Streptomyces. We elucidated possible regulatory functions of one of the identified genes, adpA19(at), most similar to archetypal adpA from model Streptomyces species, in a series of expression experiments. Introduction of adpA19 at under control of its own promoter on moderate copy number vector pKC1139 into NRRL-B16726 had no influence on antibiotic production and sporulation. Introduction of adpA19 at into Streptomyces coelicolor M145 and several S. ghanaensis strains had major influence on antibiotic production by these bacteria. Finally, adpA19 at expression in a set of soil actinomycete isolates led to induction of synthesis of antibiotic compounds. Our data point to pleiotropic regulatory role of adpA19(at), warranting its use as a tool to manipulate secondary metabolome of actinomycetes.

Cultivable actinomycetes from rhizosphere of birch (Betula pendula) growing on a coal mine dump in Silets, Ukraine.

Five actinomycete strains were isolated from the rhizosphere of birch, one of a few native tree forms capable of thriving on the upper level of a coal mine dump near the village of Silets (Lvivska region, Ukraine). No such strains were isolated from surrounding gangue, or from nearby grass Calamagrostis epigeios. Using 16S rDNA sequencing and analysis of cell wall aminoacids, four of these strains were shown to belong to genus Streptomyces and one to be Amycolatopsis. The isolates were able to produce siderophores and antibacterial compounds. In comparison to the reference strain Streptomyces coelicolor M145, certain rhizospheric isolates displayed somewhat increased survival in the presence of copper, iron(III), or chromium(VI) salts. The Amycolatopsis isolate was also shown to accumulate significant quantities of heavy metals from waste extracts. Possible roles of the described strains in coal mine dump ecology are discussed.

Influence of transition metals on Streptomyces coelicolor and S. sioyaensis and generation of chromate-reducing mutants.

Bacteria-assisted bioremediation is widely recognized as a low-cost method to minimize the consequences of soil pollution with toxic metals originating from industrial sites. Strains used in bioremediation have to deal with high metal load via biosorption, reduction, bioprecipitation, metal sequestration, and/or chelation. Actinobacteria, and streptomycetes in particular, are considered a perspective group for bioremediation as natural soil inhabitants with extensive secondary metabolism. Nevertheless, there is no reference information on survival of the model streptomycetes in the presence of the most abundant metal pollutants. Also, there are no reports describing the selection approaches towards improvement of bioremediation properties. In this work, the resistance of Streptomyces coelicolor M145 and Streptomyces sioyaensis Lv81 to certain transition metals and their growth under different pH values are described for the first time. Spontaneous chromate-resistant S. sioyaensis Lv81-138 strain was selected in the course of this work. Strain Lv81-138 is the most efficient actinobacterial Cr(VI) reducer reported so far, capable of converting 12 mmol/L of Cr(VI) into Cr(III) in a medium supplemented with 50 mmol/L K2CrO4.