Genus Streptomyces Research Articles

Impact of Nitrogen-Containing Compounds on Secondary Metabolism in Streptomyces spp.—A Source of Metabolic Engineering Strategies

Actinobacteria from the genus Streptomyces feature complex primary and secondary metabolism, developmental cycle, and ability to produce a variety of natural products. These soil bacteria are major producers of antibiotics and other bioactive compounds and have been extensively investigated due to the medical and industrial relevance of Streptomyces-derived secondary metabolites. However, the genetic toolbox for Streptomyces engineering as well as yield optimization strategies for the production of relevant metabolites are limited. On the one hand, the genetic potential of these organisms has not been fully utilized due to many “silent” or poorly expressed biosynthetic gene clusters, whose activation depends on environmental stimuli and nutrient availability. On the other hand, these GC-rich Gram-positive bacteria are difficult to manipulate, and traditional genetic manipulation strategies are time-consuming and have low efficiency. Recent studies of Streptomyces metabolism and genomes provided new insights into possibilities to overcome these challenges. In this review, advances and approaches for Streptomyces manipulations and secondary metabolite production optimization are discussed. Special focus is given to understanding the interplay between primary and secondary metabolism in Streptomyces and the supply of nitrogen-containing compounds into secondary metabolism. Existing strategies to manipulate cellular metabolism in Streptomyces are reviewed.

Streptomyces as a promising biological control agents for plant pathogens.

Plant diseases caused by pathogenic microorganisms in agriculture present a considerable obstacle, resulting in approximately 30-40% crop damage. The use of conventional techniques to manage these microorganisms, i.e., applying chemical pesticides and antimicrobials, has been discovered to have adverse effects on human health and the environment. Furthermore, these methods have contributed to the emergence of resistance among phytopathogens. Consequently, it has become imperative to investigate natural alternatives to address this issue. The Streptomyces genus of gram-positive bacteria is a potentially viable natural alternative that has been extensively researched due to its capacity to generate diverse antimicrobial compounds, such as metabolites and organic compounds. Scientists globally use diverse approaches and methodologies to extract new bioactive compounds from these bacteria. The efficacy of bioactive compounds in mitigating various phytopathogens that pose a significant threat to crops and plants has been demonstrated. Hence, the Streptomyces genus exhibits potential as a biological control agent for combating plant pathogens. This review article aims to provide further insight into the Streptomyces genus as a source of antimicrobial compounds that can potentially be a biological control against plant pathogens. The investigation of various bioactive compounds synthesized by this genus can enhance our comprehension of their prospective utilization in agriculture.

Streptomyces changanensis sp. nov. Isolated from Soil in China.

An aerobic, Gram-positive, and non-motile actinomycete, designated HL-66T, was isolated from a soil sample collected in the Meridian Valley, Shaanxi Province, China. Morphological, chemotaxonomic, and phylogenetic characteristics showed a high similarity to the genus Streptomyces. Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbour of HL-66T were Streptomyces lavendofoliae NBRC 12882T (99.17%), Streptomyces gobitricini NBRC 15419T (99.03%) and Streptomyces roseolilacinus NBRC 12815T (98.96%). Genome relatedness indexes revealed that the average nucleotide identity and digital DNA-DNA hybridization values between HL-66T and its closest phylogenomic relative (S. roseolilacinus JCM 4335T) were 88.61% and 32.10%, respectively. The cell-wall peptidoglycan contains LL-diaminopimelic acid. Predominant menaquinones are MK-9 (H6), MK-9(H4) and MK-9(H8). The major cellular fatty acids were iso-C16:0, anteiso-C15:0, iso-C16:1 H, and C16:1 ω7c. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, and an unknown phospholipid. Based on phylogenetic analyses, genome-genome distance calculation, and average nucleotide identity, strain HL-66T represents a novel species of the genus Streptomyces. Therefore, a new species Streptomyces changanensis sp. nov. is proposed with strain HL-66T (= CGMCC 22674 = JCM 35800) as the type strain.

Comparative genomic and metabolomic study of three Streptomyces sp. differing in biological activity.

The Streptomyces genus is known to produce many specialized metabolites of value for medicine, but the potential of these metabolites in agronomy remains largely unexplored. In this study, we investigated three phylogenetically closely related Streptomyces strains (B5, B91, and B135) isolated from three distinct soil samples in Sudan. Despite belonging to the same species, these strains exhibited different ranges of Phytophthora infestans inhibition. The objective of this work was to identify the active compound(s) responsible for the inhibition of P. infestans and of other plant pathogens by comparing the genomes and metabolomes of the three strains which showed distinct activity patterns: B5 was the strongest inhibitor of oomycetes, B5 and B91 both inhibited most fungi and B135 was the only strain showing antibacterial activity. Our comparative genomic and metabolomic analysis identified borrelidin as the bioactive compound underlying B5's strong anti-oomycete activity and highlighted a few other metabolites as putative candidates underlying the strains' antifungal and antibacterial activities. This study illustrates the power of comparative genomics and metabolomics on phylogenetically closely related strains of differing activities to highlight bioactive compounds that could contribute to new sustainable crop protection strategies.

Transposon-based identification of genes involved in the rimocidin biosynthesis in Streptomyces rimosus M527.

The transposon mutagenesis strategy has been employed to generate random insertion mutants and analyze the correlation between genes and secondary metabolites in the genus Streptomyces. In this study, our primary objective was to identify an unknown gene involved in rimocidin biosynthesis and elucidate its role in rimocidin production in Streptomyces rimosus M527. To achieve this, we established a random mutant library of S. rimosus M527 using a Tn5 transposon-mediated random mutagenesis strategy. Among the 137 isolated mutants, M527-G10 and M527-W5 exhibited the most significant variations in antagonistic activity against the plant pathogenic fungus Fusarium oxysporum f. sp. cucumerinum. Specifically, M527-G10 displayed a 72.93% reduction, while M527-W5 showed a 49.8% increase in rimocidin production compared to the wild-type (WT) strain S. rimosus M527. Subsequently, we employed a plasmid rescue strategy to identify the insertion loci of the transposon in the genomes of mutants M527-G10 and M527-W5, revealing a response regulator transcription factor (rrt) and a hypothetical protein (hyp), respectively. The roles of rrt and hyp in rimocidin biosynthesis were determined through gene deletion, overexpression in the WT strain, and complemented expression in the transposon mutants. Notably, the gene-deletion mutants M527-ΔRRT and M527-ΔHYP exhibited similar behavior in rimocidin production compared to the corresponding transposon mutants M527-G10 and M527-W5, suggesting that transposon insertions in genes rrt and hyp led to alterations in rimocidin production. Furthermore, both gene deletion and overexpression of rrt and hyp had no discernible effects on cell growth. These results reveal that genes rrt and hyp have positive and negative impacts on rimocidin production in S. rimosus M527, respectively.

Profile of PKS and NRPS Gene Clusters in the Genome of Streptomyces cellostaticus NBRC 12849T

Polyketides and nonribosomal peptides are major secondary metabolites in members of the genus Streptomyces. Streptomyces cellostaticus is a validly recognized species and the type strain produces cellostatin. However, little is known about whether it has the potential to produce diverse polyketides and nonribosomal peptides. Here, we sequenced the whole genome of S. cellostaticus NBRC 12849T and surveyed polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters in the genome. The genome encoded 12 PKS, one NRPS and eight hybrid PKS/NRPS gene clusters. Among the 21 gene clusters, products of 10 gene clusters were annotated to be an annimycin congener, fuelimycins, lankamycin, streptovaricin, spore pigment, flaviolin, foxicin, blasticidin, lankacidin and an incarnatapeptine congener via our bioinformatic analysis. Although the other clusters were orphan and their products were unknown, five of them were predicted to be compounds derived from two independent diketides, a tridecaketide, a triketide and a tetraketide with a cysteine residue, respectively. These results suggest that S. cellostaticus is a source of diverse polyketides and hybrid polyketide/nonribosomal peptides, including unknown and new secondary metabolites.

Large-scale Bioinformatic Study of Graspimiditides and Structural Characterization of Albusimiditide.

Graspetides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that exhibit an impressive diversity in patterns of side chain-to-side chain ω-ester or ω-amide linkages. Recent studies have uncovered a significant portion of graspetides to contain an additional post-translational modification involving aspartimidylation catalyzed by an O-methyltransferase, predominantly found in the genomes of actinomycetota. Here, we present a comprehensive bioinformatic analysis focused on graspetides harboring aspartimide, for which we propose the name graspimiditides. From protein BLAST results of 5000 methyltransferase sequences, we identified 962 unique putative graspimiditides, which we further classified into eight main clusters based on sequence similarity along with several smaller clusters and singletons. The previously studied graspimiditides, fuscimiditide, and amycolimiditide, are identified in this analysis; fuscimiditide is a singleton, while amycolimiditide is in the fifth largest cluster. Cluster 1, by far the largest cluster, contains 641 members, encoded almost exclusively in the Streptomyces genus. To characterize an example of a graspimiditide in Cluster 1, we conducted experimental studies on the peptide from Streptomyces albus J1074, which we named albusimiditide. By tandem mass spectrometry, hydrazinolysis, and amino acid substitution experiments, we elucidated the structure of albusimiditide to be a large tetracyclic peptide with four ω-ester linkages generating a stem-loop structure with one aspartimide. The ester cross-links form 22-, 46-, 22-, and 44-atom macrocycles, the last of which, the loop, contains the enzymatically installed aspartimide. Further in vitro experiments revealed that the aspartimide hydrolyzes in a 3:1 ratio of isoaspartate to aspartate residues. Overall, this study offers comprehensive insight into the diversity and structural features of graspimiditides, paving the way for future investigations of this unique class of natural products.

Comparative analysis of Actinobacteria phage-plasmids and their transduction potential

The genus Streptomyces is the most extensively studied group within actinobacteria, which are widely used for the production of antibiotics and other metabolites. Streptomyces bacteriophages attract a lot of interest to study phage-host coevolution. One of the probable interactions is a bacteriophage-mediated horizontal transfer of genes encoding bacterial metabolites, which are important for humans. In this study, a search for Streptomyces bacteriophages having capacities necessary for efficient horizontal transfer was performed. Groups of bacteriophages of actinobacteria and their plasmids with relatively long GC-rich sequences containing both genes related to viral morphogenesis and plasmid-associated genes were revealed by comparative genome analysis. In one of these groups, homologs of proteins of DNA packaging into a capsid of Punavirus genus phages, that representatives are capable to perform a horizontal transfer of genes with high frequency were identified. Taking it into account, as well as the peculiarities of their genomic structure, horizontal gene transfer by this group of viruses and plasmids was assumed to occur. Considering the genome length and GC-content, it is thought that these viruses could be useful for producers construction. Moreover, some given examples showing the chimerical origin of phage-plasmids allow suggesting that recombination events between considered phages-plasmids occur at high frequency. New representatives of viruses with low similarity to known phage genomes were also detected among plasmids. A wide diversity of actinobacterial phage-plasmids that is related to their variability and a probable existence of a great number of sequences of this type of viruses in databases were found out.

Comparative genomics reveals environmental adaptability and antimicrobial activity of a novel Streptomyces isolated from soil under black Gobi rocks.

A novel Streptomyces strain, designated 3_2T, was isolated from soil under the black Gobi rock sample of Northwest China. The taxonomic position of this strain was revealed by a polyphasic approach. Comparative analysis of the 16S rRNA gene sequences indicated that 3_2T was closely related to the members of the genus Streptomyces, with the highest similarity to Streptomyces rimosus subsp. rimosus CGMCC 4.1438 (99.17%), Streptomyces sioyaensis DSM 40032 (98.97%). Strain 3_2T can grow in media up to 13% NaCl. The genomic DNA G + C content of strain 3_2T was 69.9%. We obtained the genomes of 22 Streptomyces strains similar to strain 3_2T, compared the average nucleotide similarity, dDDH and average amino acid identity, and found that the genomic similarity of the new isolate 3_2T to all strains was below the threshold for interspecies classification. Chemotaxonomic data revealed that strain 3_2T possessed MK-9 (H6) and MK-9 (H8) as the major menaquinones. The cell wall contained LL-diaminopimelic acid (LL-DAP) and the whole-cell sugars were ribose and glucose. The major fatty acid methyl esters were iso-C16:0 (23.6%) and anteiso-C15:0 (10.4%). The fermentation products of strain 3_2T were inhibitory to Staphylococcus aureus and Bacillus thuringiensi. The genome of 3_2T was further predicted using anti-smash and the strain was found to encode the production of 41 secondary metabolites, and these gene clusters may be key to the good inhibitory activity exhibited by the strain. Genomic analysis revealed that strain 3_2T can encode genes that produce a variety of genes in response to environmental stresses, including cold shock, detoxification, heat shock, osmotic stress, oxidative stress, and these genes may play a key role in the harsh environment in which the strain can survive. Therefore, this strain represents a novel Streptomyces species, for which the name Streptomyces halobius sp. nov. is proposed. The type strain is 3_2T (= JCM 34935T = GDMCC 4.217T).

Genome mining reveals secondary metabolites of Antarctic bacterium Streptomyces albidoflavus related to antimicrobial and antiproliferative activities.

The urgent need for new antimicrobials arises from antimicrobial resistance. Actinobacteria, especially Streptomyces genus, are responsible for production of numerous clinical antibiotics and anticancer agents. Genome mining reveals the biosynthetic gene clusters (BGCs) related to secondary metabolites and the genetic potential of a strain to produce natural products. However, this potential may not be expressed under laboratory conditions. In the present study, the Antarctic bacterium was taxonomically affiliated as Streptomyces albidoflavus ANT_B131 (CBMAI 1855). The crude extracts showed antimicrobial activity against both fungi, Gram-positive and Gram-negative bacteria and antiproliferative activity against five human tumor cell lines. Whole-genome sequencing reveals a genome size of 6.96Mb, and the genome mining identified 24 BGCs, representing 13.3% of the genome. The use of three culture media and three extraction methods reveals the expression and recovery of 20.8% of the BGCs. The natural products identified included compounds, such as surugamide A, surugamide D, desferrioxamine B + Al, desferrioxamine E, and ectoine. This study reveals the potential of S. albidoflavus ANT_B131 as a natural product producer. Yet, the diversity of culture media and extraction methods could enhance the BGCs expression and recovery of natural products, and could be a strategy to intensify the BGC expression of natural products.

Insects and their antibiotic-producing bacteria

Many, if not all, plants and animals form mutually beneficial symbioses (mutualisms) with microbes and a subset of these mutualisms are defensive, in which the host provides food and housing in return for defence against disease. These symbioses typically involve antibiotic-producing bacteria, the best known of which are filamentous actinomycetes in the genera Streptomyces and Pseudonocardia and unicellular species in the genus Pseudomonas. Such mutualisms are likely to be widespread in nature, but they are best characterised in insects, which provide experimentally tractable models for studying symbiosis and microbiome formation because they typically host less complex microbial communities. Here, we examine the mutualisms formed between insects and antibiotic-producing bacteria using well-characterised examples, including digger wasps and their endosymbiotic Streptomyces species, attine ants and their mutualist Pseudonocardia species and Paederus beetles with their pederin-producing Pseudomonas species. We also discuss how searching such symbiotic niches can give insights into the evolution and functions of microbial specialised metabolites and provide new platforms for antibiotic discovery.

A peptide encoded by a highly conserved gene belonging to the genus Streptomyces shows antimicrobial activity against plant pathogens.

The genus Streptomyces has been unceasingly highlighted for the versatility and diversity of the antimicrobial agents they produce. Moreover, it is a heavily sequenced taxon in the phylum Actinobacteria. In this study, 47 sequence profiles were identified as proteins highly conserved within the genus Streptomyces. Significant hits to the 38 profiles were found in more than 2000 Streptomyces genomes, 11 of which were further conserved in more than 90% of Actinobacterial genomes analyzed. Only a few genes corresponding to these sequence profiles were functionally characterized, which play regulatory roles in the morphology and biosynthesis of antibiotics. Here a highly conserved sequence, namely, SHC-AMP (Streptomyces highly conserved antimicrobial peptide), which exhibited antimicrobial activity against bacterial and fungal plant pathogens, was reported. In particular, Arabidopsis thaliana was effectively protected against infection with Pseudomonas syringae pv. tomato DC3000 by treatment with this peptide. Results indicated the potential application of this peptide as an antimicrobial agent for control of plant diseases. Our results suggest putative target genes for controlling Streptomyces spp., including the one exhibiting antimicrobial activity against a wide range of phytopathogens.

Streptomyces silvisoli sp. nov., a polyene producer, and Streptomyces tropicalis sp. nov., two novel actinobacterial species from peat swamp forests in Thailand.

Two novel actinobacterial strains, designated RB6PN23T and K1PA1T, were isolated from peat swamp soil samples in Thailand and characterized using a polyphasic taxonomic approach. The strains were filamentous Gram-stain-positive bacteria containing ll-diaminopimelic acid in their whole-cell hydrolysates. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strain RB6PN23T was most closely related to Streptomyces rubrisoli (99.1 % sequence similarity) and Streptomyces ferralitis (98.5%), while strain K1PA1T showed 98.8 and 98.7% sequence similarities to Streptomyces coacervatus and Streptomyces griseoruber, respectively. However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were below the species-level thresholds (95-96 % ANI and 70 % dDDH). The genomes of strains RB6PN23T and K1PA1T were estimated to be 7.88 Mbp and 7.39 Mbp in size, respectively, with DNA G+C contents of 70.2 and 73.2 mol%. Moreover, strains RB6PN23T and K1PA1T encode 37 and 24 putative biosynthetic gene clusters, respectively, and in silico analysis revealed that these new species have a high potential to produce unique natural products. Genotypic and phenotypic characteristics confirmed that strains RB6PN23T and K1PA1T represented two novel species in the genus Streptomyces. The names proposed for these strains are Streptomyces silvisoli sp. nov. (type strain RB6PN23T=TBRC 17040T=NBRC 116113T) and Streptomyces tropicalis sp. nov. (type strain K1PA1T=TBRC 17041T=NBRC 116114T). Additionally, a giant linear polyene compound, neotetrafibricin A, exhibiting antifungal activity in strain RB6PN23T, was identified through HPLC and quadrupole time-of-flight MS analysis. The crude extract from the culture broth of strain RB6PN23T exhibited strong antifungal activity against Fusarium verticillioides, Fusarium fujikuroi and Bipolaris zeicola. This finding suggests that strain RB6PN23T could be a promising candidate for biological control of fungal diseases.

Enzymes of microorganisms. Proteases of lactic acid bacterias

The work is devoted to the enzymes of microorganisms. This review article presents the characteristics of microbial enzymes, their classifications according to various parameters. The study examines the role of microbial enzymes in various areas of human life. Enzymes are involved in the biochemical processes of microorganisms for their protection, reproduction, and growth. Enzyme producers are various taxonomic groups of bacteria, filamentous fungi, actinomycetes and yeasts. The article describes hydrolytic enzymes, reveals the importance of the protease enzyme involved in various processes with microorganisms. The main producers of proteolytic enzymes are bacteria of the genus Bacillus, Lactobacillus, Streptococcus, Micrococcus, Pseudomonas, fungi of the genus Aspergillus, Penicillium, Blakeslea, actynomicetes of the genus Streptomyces, Actinomyces. Particular attention is paid to lactic acid bacteria. The significance of the use of protease in the biotechnological industry, in particular, for the development of preparations, starter cultures, bioadditives, and functional food products with desired properties, is shown. The article mentions the results of a study of the proteolytic activity of cultures of microorganisms, obtained by me and my colleagues. The objects of study were bacilli, yeast, fungi and lactic acid bacteria.To assess proteolytic activity, in vitro methods, chromatographic and other methods are used.

Streptomyces fuscus sp. nov., a brown-black pigment producing actinomycete isolated from dry mudflat sand.

A novel Gram-stain-positive, aerobic actinobacterial strain, designated GXMU-J15T, was isolated from dry mudflat sand. A polyphasic approach was employed for its taxonomic characterization. The strain developed extensively branched yellowish white to light yellow substrate mycelia and white aerial mycelia, and produced smooth cylindrical spores in a loose straight spore chain on International Streptomyces Project 2-7 agar media. Strain GXMU-J15T grew at 20-50 °C (optimum, 35 °C), at pH 5.0-8.0 (optimum, pH 7.0) and in the presence of 0-8 % (w/v) NaCl. Analysis of 16S rRNA gene sequences indicated that strain GXMU-J15T represents a member of the genus Streptomyces. Strain GXMU-J15T showed the highest 16S rRNA gene sequence similarity to Streptomyces lusitanus CGMCC 4.1745T (99.1 %) and Streptomyces thermocarboxydus CGMCC 4.1883T (98.8 %). Phylogenetic tree analysis based on multilocus sequence analysis (MLSA) and whole genome sequence construction revealed that strain GXMU-J15T was most closely related to Streptomyces cupreus PSKA01T, Streptomyces cinnabarinus DSM 40467T and Streptomyces davaonensis JCM 4913T. The MLSA and genome-to-genome distances between strain GXMU-J15T and its relatives were 0.0418, 0.0443 and 0.0485 and 0.1237, 0.1188 and 0.1179, respectively. The results of orthologous average nucleotide identity and digital DNA-DNA hybridization analysis corroborated the results of the MLSA and whole genome sequence evolution analysis, indicating that the novel isolate represents a distinct species of the genus Streptomyces. The whole-cell sugars of strain GXMU-J15T were xylose, glucose and galactose. The characteristic diamino acid in the cell-wall hydrolysate was ll-diaminopimelic acid. The lipids contained diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol, phosphatidylglycerides, phosphatidylcholine, two phospholipids of an unknown structure containing glucosamine, one unknown phospholipid and two unknown lipids. The major cellular fatty acid components were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The main respiratory quinone types were MK-9(H6) and MK-9(H8). The whole genome size of strain GXMU-J15T was 8.68 Mbp, with 71.23 mol% G+C content. Genomic analysis indicated that strain GXMU-J15T has the potential to synthesize polyketides, terpenes and a series of important antibiotics besides the gene cluster for melanin synthesis. Based on these genotypic and phenotypic data, strain GXMU-J15T is proposed to represent a new species of the genus Streptomyces named Streptomyces fuscus sp. nov. The type strain is GXMU-J15T (=MCCC 1K08211T=JCM 35917T).

Bioactivity Features of Novel Actinobacteria Isolated from Lichen and Orchid Plant

A total of 10 actinobacterial strains were isolated from a lichen and an orchid species by employing a selective isolation procedure for actinobacteria. Antimicrobial activities of the isolates were evaluated against Aspergillus niger ATCC 16404, Candida albicans ATCC 10231, Enterococcus faecalis ATCC 29212, Bacillus subtilis ATCC 6633, Escherichia coli ATCC 25922, Klebsiella pneumoniae ATCC 700603, Pseudomonas aeroginosa ATCC 27853, Salmonella enterica ATCC 13311, Staphylococcus aureus ATCC 29213 and Listeria monocytogenes NCTC 5348. Out of the 10 isolates, eight showed antimicrobial activity against at least one pathogen. For molecular identification of the strains, 16S rRNA gene sequence analysis was performed. The pairwise comparison of the 16S rRNA gene sequences of the strains with the databases showed that the strains are members of the genus Streptomyces by sharing 98.9 – 100% gene sequence similarities. Phylogenetic relationships of the strains within the genus Streptomyces were revealed by maximum likelihood and maximum parsimony phylogenetic trees. The results revealed that unexplored environmental habitats like lichens and plant tissues may represent a potential reservoir for novel actinobacteria with promising bioactivity features.

Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions

Climate change increases the frequency and intensity of drought events, affecting soil functions including carbon sequestration and nutrient cycling, which are driven by growing microorganisms. Yet we know little about microbial responses to drought due to methodological limitations. Here, we estimate microbial growth rates in montane grassland soils exposed to ambient conditions, drought, and potential future climate conditions (i.e., soils exposed to 6 years of elevated temperatures and elevated CO2 levels). For this purpose, we combined 18O-water vapor equilibration with quantitative stable isotope probing (termed ‘vapor-qSIP’) to measure taxon-specific microbial growth in dry soils. In our experiments, drought caused >90% of bacterial and archaeal taxa to stop dividing and reduced the growth rates of persisting ones. Under drought, growing taxa accounted for only 4% of the total community as compared to 35% in the controls. Drought-tolerant communities were dominated by specialized members of the Actinobacteriota, particularly the genus Streptomyces. Six years of pre-exposure to future climate conditions (3 °C warming and + 300 ppm atmospheric CO2) alleviated drought effects on microbial growth, through more drought-tolerant taxa across major phyla, accounting for 9% of the total community. Our results provide insights into the response of active microbes to drought today and in a future climate, and highlight the importance of studying drought in combination with future climate conditions to capture interactive effects and improve predictions of future soil-climate feedbacks.

Streptomyces rugosispiralis sp. nov., a Novel Actinobacterium Isolated from Peat Swamp Forest Soil That Produces Ansamycin Derivatives and Nocardamines.

Actinomycetes, especially the genus Streptomyces, are one of the most promising sources of bioactive natural products. In this study, a novel Streptomyces strain, RCU-064T, was isolated from a soil sample collected from a peat swamp forest in Thailand. Strain RCU-064T showed the highest 16S rRNA gene sequence similarity (99.06%) with Streptomyces malaysiensis NBRC 16446T. Based on a polyphasic approach, strain RCU-064T represents a novel species of the genus Streptomyces, for which the name Streptomyces rugosispiralis sp. nov. is proposed. The chemical isolation of the crude ethyl acetate extracts of the strain led to the isolation of six compounds: (1) geldanamycin, (2) 17-O-demethylgeldanamycin, (3) reblastatin, (4) 17-demethoxyreblastatin, (5) nocardamine, and (6) dehydroxynocardamine. These compounds were evaluated for their biological activities. All compounds showed no antimicrobial activity against tested microorganisms used in this study. Compounds (1)-(4) displayed cytotoxic activity against the NCI-H187 cell line, with IC50 values ranging from 0.045-4.250 µg/mL. Cytotoxicity against the MCF-7 cell line was found in compounds (1) and (3) with IC50 values of 3.51 and 1.27 µg/mL, respectively. Compounds (5) and (6) exhibited cytotoxicity only against Vero cells (IC50 of 16.57 µg/mL) and NCI-H187 cells (IC50 of 13.96 µg/mL), respectively. These results indicate that peat swamp forest soil remains a promising reservoir of novel actinomycetes capable of producing bioactive natural products.

Streptomyces sp. VITGV156 (MCC 4965), a quinoline producing Streptomyces

The genus Streptomyces is renowned for its ability to synthesize a wide range of secondary metabolites, encompassing antimicrobial, anticancer, antiviral, antioxidant, immunosuppressant and antimalarial properties. In this study, we focused on Streptomyces sp. VITGV156 to explore its potential in producing quinoline, a secondary metabolite, leveraging the species' extensive biosynthetic gene repertoire. The complete genome of Streptomyces sp. VITGV156 was sequenced using Illumina technology and NextSeq. Genome analysis unveiled 29 Biosynthetic Gene Clusters (BGCs), including 7 PKS (Polyketide Synthases) and 5 terpenes, responsible for secondary metabolite production. The crude extract of VITGV156 was subjected to GC-MS analysis, revealing the presence of 30 distinct compounds, 15 of which exhibited antimicrobial activity. Notably, quinoline carboxylic acid was detected at a retention time of 17.628 min. Given the promising antimicrobial activity displayed by the crude extract of Streptomyces sp. VITGV156, further investigations are planned to gain deeper insights into its secondary metabolites.

Streptomyces argyrophyllae sp. nov., isolated from the rhizosphere soil of Cathaya argyrophylla.

Strain Jing01T, a novel actinomycete from rhizosphere soil of Cathaya argyrophylla, was identified using a polyphasic approach. 16S rRNA gene sequence analysis of strain Jing01T revealed that it was a member of the genus Streptomyces and shared 99.03%, 99.03%, 98.96%, 98.89%, 98.83%, 98.82%, 98.76%, 98.74%, 98.73%, 98.69% and 98.68% similarities to Streptomyces rochei NRRL B-2410T, Streptomyces naganishii NBRC 12892T, Streptomyces rubradiris JCM 4955T, Streptomyces anandii NRRL B-3590T, Streptomyces aurantiogriseus NBRC 12842T, Streptomyces mutabilis NBRC 12800T, Streptomyces rameus LMG 20326T, Streptomyces djakartensis NBRC 15409T, Streptomyces bangladeshensis JCM 14924T, Streptomyces andamanensis KCTC 29502T and Streptomyces tuirus NBRC 15617T, respectively. In phylogenetic trees constructed based on 16S rRNA gene sequences, strain Jing01T generated a separate branch at the middle of the clade, suggesting it could be a potential novel species. In phylogenomic tree, strain Jing01T was related to S. rubradiris JCM 4955T. In phylogenetic trees based on the gene sequences of atpD, gyrB, recA, rpoB and trpB, strain Jing01T was related to S. bangladeshensis JCM 14924T and S. rubradiris JCM 4955T. Whereas, the multilocus sequence analysis distance, average nucleotide identity and DNA-DNA hybridization values between them were much less than the species-level thresholds. This conclusion was further supported by phenotypic and chemotaxonomic analysis. Consequently, strain Jing01T represents a new Streptomyces species, for which the proposed name is Streptomyces argyrophyllae sp. nov. The type strain is Jing01T (= MCCC 1K05707T = JCM 35923T).