Phylogenetic study of the species within the family Streptomycetaceae

Manure-Amended One-Year-Reclamation Promoted Soil Bacterial Phylotypic and Phenotypic Shifts in a Typical Coal-Mining Area

The initial variations in soil bacteria at the very beginning of reclamation still remains unclear. This study investigates the impact on bacterial communities of eight different treatments, including uncultivated land, unfertilized cultivation, chemical fertilizer, chemical fertilizer + bacterial fertilizer, manure, manure + bacterial fertilizer, manure + chemical fertilizer, and manure + chemical fertilizer + bacterial fertilizer, during the short-term reclamation of coal-mining soils. The results showed that total nitrogen, available phosphorus, soil organic carbon, microbial biomass carbon, and alkaline phosphatase activity were significantly increased in all fertilization treatments compared to uncultivated land (p < 0.05). All fertilization treatments other than chemical fertilizer harbored significantly higher activities of urease, catalase, and invertase than unfertilized cultivation (p < 0.05). The bacterial communities structures in manure-amended treatments significantly differed in uncultivated land and unfertilized cultivation and were phylotypically shifted from oligotrophic to Actinobacteria-dominant copiotrophic traits, accompanied with phenotypic succession of the enriching characteristics of Gram-positive, biofilms formation, and stress tolerance. The co-occurrence network in manure-amended treatments harbored a simple co-occurrence network, indicating more productive soils than in no-manure treatments. Manure amendment, total nitrogen, microbial biomass carbon, invertase, catalase, and soil moisture were the key driving factors. Our study underscores the bacterial initialization characteristics promoted by manure at the very beginning of coal-mining reclamation.

Polyphasic taxonomic description of Streptomyces okerensis sp. nov. and Streptomyces stoeckheimensis sp. nov. and their biotechnological potential

Streptomyces strains DSM 116494T and DSM 116496T were isolated from sediment samples of the River Oker in Braunschweig, Germany, and subjected to a polyphasic taxonomic study and genome mining for specialized secondary metabolites. Phenotypic, genetic and genomic data confirmed the assignment of these strains to the Streptomyces genus. Pairwise 16S rRNA gene sequence similarity values between the strains and validly named Streptomyces species reached 99.5 and 99.7% for strains DSM 116494T and DSM 116496T, respectively. Genome-based phylogeny demonstrated that Streptomyces pilosus and Streptomyces griseoflavus species were the close relatives to strain DSM 116494T, while Streptomyces vinaceus species was the nearest neighbour to strain DSM 116496T. Digital DNA-DNA hybridization and average nucleotide identity comparisons of the genomic sequence of the strains and their close phylogenomic relatives revealed that values were below the determined threshold of 70 and 95-96% for prokaryotic species demarcation, respectively. The strains were distinguished from their close neighbours based on biochemical, chemotaxonomic and enzymatic data. Given these results, the strains merit being affiliated to novel species within the genus Streptomyces, for which the names Streptomyces okerensis sp. nov. (=OG2.3T=DSM 116494T=KCTC 59408T) and Streptomyces stoeckheimensis sp. nov. (=OG3.14T=DSM 116496T=KCTC 59410T) are proposed. Strains DSM 116494T and DSM 116496T harboured several biosynthetic gene clusters encoding potentially novel antimicrobial and anticancer compounds. Crude extracts of strains DSM 116494T and DSM 116496T inhibited the growth of Gram-negative bacteria (Escherichia coli ΔtolC, Proteus vulgaris) and a multi-drug-resistant Gram-positive, Staphylococcus aureus.

Genome Mining Analysis Uncovers the Previously Unknown Biosynthetic Capacity for Secondary Metabolites in Verrucomicrobia

Bacteria of the phylum Verrucomicrobia is widely distributed in diverse ecological environments. Their limited cultivability has greatly caused the significant knowledge gap surrounding their secondary metabolites and their mediating ecological functions. This study delved into the diversity and novelty of secondary metabolite biosynthetic gene clusters (BGCs) of Verrucomicrobia by employing a gene-first approach to investigate 2323 genomes. A total of 7552 BGCs, which encompassed 3744 terpene, 805 polyketide, 773 non-ribosomal peptide gene clusters, and 1933 BGCs of other biosynthetic origins, were identified. They were further classified into 3887 gene cluster families (GCFs) based on biosynthetic gene similarity clustering, of which only six GCFs contained reference biosynthetic gene clusters in the Minimum Information about a Biosynthetic Gene Cluster (MIBiG), indicating the striking novelty of secondary metabolites in Verrucomicrobia. Notably, 37.8% of these gene clusters were harbored by unclassified species of Verrucomicrobia phyla, members of which were highly abundant in soil environments. Furthermore, our comprehensive analysis also revealed Luteolibacter and Methylacidiphilum as the most prolific genera in terms of BGC abundance and diversity, with the discovery of a conservative and new NRPS-PKS BGC in Luteolibacter. This work not only unveiled the biosynthetic potential and genetic diversity of secondary metabolites of Verrucomicrobia but also provided a fresh insight for the exploration of new bioactive compounds.

Genomic and Untargeted Metabolomic Analysis of Secondary Metabolites in the Streptomyces griseoaurantiacus Strain MH191 Shows Media-Based Dependency for the Production of Bioactive Compounds with Potential Antifungal Activity

Streptomyces species can form beneficial relationships with hosts as endophytes, including the phytopathogen-inhibiting strain, Streptomyces griseoaurantiacusMH191, isolated from wheat plants. Using genomic characterization and untargeted metabolomics, we explored the capacity of strain MH191 to inhibit a range of fungal phytopathogens through the production of secondary metabolites. Complete genome assembly of strain MH191 predicted 24 biosynthetic gene clusters. Secondary metabolite production was assessed following culture on six different media, with the detection of 205 putative compounds. Members of the manumycin family, undecylprodigiosin, and desferrioxamine were identified as the predominant metabolites. Antifungal activity was validated for undecylprodigiosin and manumycin. These compounds were produced from different BGCs, which showed similarity to asukamycin, undecylprodigiosin, and FW0622 gene clusters, respectively. The growth of strain MH191 on different media illustrated the metabolic regulation of these gene clusters and the strain's extended chemical potential, with the asukamycin gene cluster alone, producing a variety of antifungal metabolites. The study highlights the extended chemical capability of strain MH191, which could be exploited as a biological control agent for designing future crop protection solutions.

In vitro and computational investigation of antioxidant and anticancer properties of Streptomyces coeruleofuscus SCJ extract on MDA-MB-468 triple-negative breast cancer cells

This study aimed to explore the antioxidant potential of the ethyl acetate extract of Streptomyces coeruleofuscus SCJ strain, along with its inhibitory effects on the triple-negative human breast carcinoma cell line (MDA-MB-468). The ethyl acetate extract's total phenolic and flavonoid contents were quantified, and its antioxidant activity was investigated using DPPH (1,1-Diphenyl-2-picrylhydrazyl), ABTS (2,2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid), and FRAP (Ferric Reducing Antioxidant Power) assays. Furthermore, the cytotoxic effect of the organic extract from Streptomyces coeruleofuscus SCJ on MDA-MB-468 cancer cells was assessed via the crystal violet assay. In tandem, a thorough computational investigation was conducted to explore the pharmacokinetic properties of the identified components of the extract, utilizing the SwissADME and pKCSM web servers. Additionally, the molecular interactions between these components and Estrogen Receptor Beta, identified as a potential target, were probed through molecular docking studies. The results revealed that ethyl acetate extract of SCJ strain exhibited remarkable antioxidant activity, with 39.899 ± 1.56% and 35.798 ± 0.082% scavenging activities against DPPH and ABTS, respectively, at 1 mg/mL. The extract also displayed significant ferric reducing power, with a concentration of 1.087 ± 0.026 mg ascorbic acid equivalents per mg of dry extract. Furthermore, a strong positive correlation (p < 0.0001) between the antioxidant activity, the polyphenol and the flavonoid contents. Regarding anticancer activity, the SCJ strain extract demonstrated significant anticancer activity against TNBC MDA-MB-468 cancer cells, with an inhibition percentage of 62.76 ± 0.62%, 62.67 ± 0.93%, and 58.07 ± 4.82% at 25, 50, and 100 µg/mL of the extract, respectively. The HPLC-UV/vis analysis revealed nine phenolic compounds: gallic acid, sinapic acid, p-coumaric acid, cinnamic acid, trans-fereulic acid, syringic acid, chloroqenic acid, ellagic acid, epicatechin. Streptomyces coeruleofuscus SCJ showed promise for drug discovery, exhibiting antioxidant and anticancer effects.

Biotechnological and pharmaceutical potential of twenty-eight novel type strains of Actinomycetes from different environments worldwide

Actinomycetes are a prolific source of bioactive natural compounds many of which are used as antibiotics or other drugs. In this study we investigated the genomic and biochemical diversity of 32 actinobacterial strains that had been deposited at the DSMZ-German Collection of Microorganisms and Cell Cultures decades ago. Genome-based phylogeny and in silico DNA-DNA hybridization supported the assignment of these strains to 26 novel species and two novel subspecies and a reclassification of a Streptomyces species. These results were consistent with the biochemical, enzymatic, and chemotaxonomic features of the strains. Most of the strains showed antimicrobial activities against a range of Gram-positive and Gram-negative bacteria, and against yeast. Genomic analysis revealed the presence of numerous unique biosynthetic gene clusters (BGCs) encoding for potential novel antibiotic and anti-cancer compounds. Strains DSM 41636T and DSM 61640T produced the antibiotic compounds A33853 and SF2768, respectively. Overall, this reflects the significant pharmaceutical and biotechnological potential of the proposed novel type strains and underlines the role of prokaryotic systematics for drug discovery. In order to compensate for the gender gap in naming prokaryotic species, we propose the eponyms for all newly described species to honour female scientists.

16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces

Streptomyces is among the most extensively studied genera of bacteria but its complex taxonomy remains contested and is suspected to contain significant species-level misclassification. Resolving the classification of Streptomyces would benefit many areas of applied microbiology that rely on an accurate ground truth for grouping of related organisms, including comparative genomics-based searches for novel antimicrobials. We survey taxonomic conflicts between 16S rRNA and whole genome-based Streptomyces classifications using 2276 publicly available Streptomyces genome assemblies and 48 981 publicly available full-length 16S rRNA Streptomyces sequences from silva, Greengenes, Ribosomal Database Project (RDP), and NCBI (National Centre for Biotechnology Information) databases. We construct a full-length 16S gene tree for 14 239 distinct Streptomyces sequences that resolves three major lineages of Streptomyces, but whose topology is not consistent with existing taxonomic assignments. We use these sequence data to delineate 16S and whole genome landscapes for Streptomyces, demonstrating that 16S and whole-genome classifications are frequently in disagreement, and that 16S zero-radius Operational Taxonomic Units (zOTUs) are often inconsistent with Average Nucleotide Identity (ANI)-based taxonomy. Our results strongly imply that 16S rRNA sequence data does not map to taxonomy sufficiently well to delineate Streptomyces species routinely. We propose that alternative marker sequences should be adopted by the community for classification and metabarcoding. Insofar as Streptomyces taxonomy has been determined or supported by 16S sequence data and may in parts be in error, we also propose that reclassification of the genus by alternative approaches may benefit the Streptomyces community.

Genomic and physiological characterization of Kitasatospora sp. nov., an actinobacterium with potential for biotechnological application isolated from Cerrado soil

An Actinobacteria - Kitasatospora sp. K002 - was isolated from the soil of Cerrado, a savanna-like Brazilian biome. Herein, we conducted a phylogenetic, phenotypic and physiological characterization, revealing its potential for biotechnological applications. Kitasatospora sp. K002 is an aerobic, non-motile, Gram-positive bacteria that forms grayish-white mycelium on solid cultures and submerged spores with vegetative mycelia on liquid cultures. The strain showed antibacterial activity against Bacillus subtilis, Pseudomonas aeruginosa and Escherichia coli. Genomic analysis indicated that Kitasatospora xanthocidica JCM 4862 is the closest strain to K002, with a dDDH of 32.8-37.8% and an ANI of 86.86% and the pangenome investigations identified a high number of rare genes. A total of 60 gene clusters of 22 different types were detected by AntiSMASH, and 22 gene clusters showed low similarity (< 10%) with known compounds, which suggests the potential production of novel bioactive compounds. In addition, phylogenetic analysis and morphophysiological characterization clearly distinguished Kitasatospora sp. K002 from other related species. Therefore, we propose that Kitasatospora sp. K002 should be recognized as a new species of the genus Kitasatospora - Kitasatospora brasiliensis sp. nov. (type strains = K002).

The Natural Products Discovery Center: Release of the First 8490 Sequenced Strains for Exploring Actinobacteria Biosynthetic Diversity

Actinobacteria, the bacterial phylum most renowned for natural product discovery, has been established as a valuable source for drug discovery and biotechnology but is underrepresented within accessible genome and strain collections. Herein, we introduce the Natural Products Discovery Center (NPDC), featuring 122,449 strains assembled over eight decades, the genomes of the first 8490 NPDC strains (7142 Actinobacteria), and the online NPDC Portal making both strains and genomes publicly available. A comparative survey of RefSeq and NPDC Actinobacteria highlights the taxonomic and biosynthetic diversity within the NPDC collection, including three new genera, hundreds of new species, and ~7000 new gene cluster families. Selected examples demonstrate how the NPDC Portal's strain metadata, genomes, and biosynthetic gene clusters can be leveraged using genome mining approaches. Our findings underscore the ongoing significance of Actinobacteria in natural product discovery, and the NPDC serves as an unparalleled resource for both Actinobacteria strains and genomes.

Glycomyces niveus sp. nov., a novel actinomycete isolated from sandy soil

A novel mycelium-forming actinomycete, designated strain NEAU-S30T, was isolated from the sandy soil of a sea beach in Shouguang city, Shandong province, PR China. The strain developed long chains of non-motile cylindrical spores with smooth surfaces on aerial mycelia. The results of a polyphasic taxonomic study indicated that NEAU-S30T represented a member of the genus Glycomyces. The results of 16S rRNA gene sequence analysis indicated that NEAU-S30T was closely related to 'Glycomycesluteolus' (98.97 % sequence similarity), Glycomycesalgeriensis (98.90 %), 'Glycomyces tritici' (98.83 %) and Glycomyces lechevalierae (98.76 %). The average nucleotide identity (ANI) values between NEAU-S30T and 'G. luteolus' NEAU-A15, G. algeriensis DSM 44727T, 'G. tritici' NEAU-C2 and G. lechevalierae DSM 44724T were 87.77, 87.53, 87.41 and 87.80 %, respectively. The digital DNA G+C content of the genomic DNA was 70.5 %. The whole-cell sugars contained ribose and xylose. The predominant menaquinones were MK-10(H2), MK-10(H4) and MK-10(H6). The predominant fatty acids were anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C15 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified glycolipid. On the basis of the results of comparative analysis of genotypic, phenotypic and chemotaxonomic data, the novel actinomycete strain NEAU-S30T (=JCM 33975T=CGMCC 4.7890T) represents the type strain of a novel species within the genus Glycomyces, for which the name Glycomyces niveus sp. nov. is proposed.

Growth Performance, Metabolomics, and Microbiome Responses of Weaned Pigs Fed Diets Containing Growth-Promoting Antibiotics and Various Feed Additives

The objective of this study was to determine the potential biological mechanisms of improved growth performance associated with potential changes in the metabolic profiles and intestinal microbiome composition of weaned pigs fed various feed additives. Three separate 42 day experiments were conducted to evaluate the following dietary treatments: chlortetracycline and sulfamethazine (PC), herbal blends, turmeric, garlic, bitter orange extract, sweet orange extract, volatile and semi-volatile milk-derived substances, yeast nucleotide, and cell wall products, compared with feeding a non-supplemented diet (NC). In all three experiments, only pigs fed PC had improved (p < 0.05) ADG and ADFI compared with pigs fed NC. No differences in metabolome and microbiome responses were observed between feed additive treatments and NC. None of the feed additives affected alpha or beta microbiome diversity in the ileum and cecum, but the abundance of specific bacterial taxa was affected by some dietary treatments. Except for feeding antibiotics, none of the other feed additives were effective in improving growth performance or significantly altering the metabolomic profiles, but some additives (e.g., herbal blends and garlic) increased (p < 0.05) the relative abundance of potentially protective bacterial genera that may be beneficial during disease challenge in weaned pigs.

Streptomyces Diversity Maps Reveal Distinct High-Specificity Biogeographical and Environmental Patterns Compared to the Overall Bacterial Diversity

Despite their enormous impact on the environment and humans, the distribution and variety of the biggest natural secondary metabolite producers, the genus Streptomyces, have not been adequately investigated. We developed representative maps from public EMP 16S rRNA amplicon sequences microbiomics data. Streptomyces ASVs were extracted from the EMP overall bacterial community, demonstrating Streptomyces diversity and identifying crucial diversity patterns. Our findings revealed that while the EMP primarily distinguished bacterial communities as host-associated or free-living (EMPO level 1), the Streptomyces community showed no significant difference but exhibited distinctions between categories in EMPO level 2 (animal, plant, non-saline, and saline). Multiple linear regression analysis demonstrated that pH, temperature, and salinity significantly predicted Streptomyces richness, with richness decreasing as these factors increased. However, latitude and longitude do not predict Streptomyces richness. Our Streptomyces maps revealed that additional samplings in Africa and Southeast Asia are needed. Additionally, our findings indicated that a greater number of samples did not always result in greater Streptomyces richness; future surveys may not necessitate extensive sampling from a single location. Broader sampling, rather than local/regional sampling, may be more critical in answering microbial biogeograph questions. Lastly, using 16S rRNA gene sequencing data has some limitations, which should be interpreted cautiously.

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).

Albocycline Is the Main Bioactive Antifungal Compound Produced by Streptomyces sp. OR6 against Verticillium dahliae

Verticillium wilt is a soil-borne fungal disease that affects olive trees (Olea europaea) and poses a serious threat to their cultivation. The causal agent of this disease is Verticillium dahliae, a pathogen that is difficult to control with conventional methods. Therefore, there is a need to explore alternative strategies for the management of Verticillium wilt. In this study, we aimed to isolate and characterize actinobacteria from the rhizosphere of olive trees that could act as potential biocontrol agents against V. dahliae. We selected a Streptomyces sp. OR6 strain based on its in vitro antifungal activity and its ability to suppress the pathogen growth in soil samples. We identified the main active compound produced by this strain as albocycline, a macrolide polyketide with known antibacterial properties and some antifungal activity. Albocycline was able to efficiently suppress the germination of conidiospores. To our knowledge, this is the first report of albocycline as an effective agent against V. dahliae. Our results suggest that Streptomyces sp. OR6, or other albocycline-producing strains, could be used as a promising tool for the biological control of Verticillium wilt.

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 6.96 Mb, 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.

Changes in the Microbial Composition of the Rhizosphere of Hop Plants Affected by Verticillium Wilt Caused by Verticillium nonalfalfae

Verticillium wilt is a devastating disease affecting many crops, including hops. This study aims to describe fungal and bacterial populations associated with bulk and rhizosphere soils in a hop field cultivated in Slovenia with the Celeia variety, which is highly susceptible to Verticillium nonalfalfae. As both healthy and diseased plants coexist in the same field, we focused this study on the detection of putative differences in the microbial communities associated with the two types of plants. Bacterial communities were characterized by sequencing the V4 region of the 16S rRNA gene, whereas sequencing of the ITS2 region was performed for fungal communities. The bacterial community was dominated by phyla Proteobacteria, Acidobacteriota, Bacteroidota, Actinobacteriota, Planctomycetota, Chloroflexi, Gemmatimonadota, and Verrucomicrobiota, which are typically found in crop soils throughout the world. At a fungal level, Fusarium sp. was the dominant taxon in both bulk and rhizosphere soils. Verticillium sp. levels were very low in all samples analyzed and could only be detected by qPCR in the rhizosphere of diseased plants. The rhizosphere of diseased plants underwent important changes with respect to the rhizosphere of healthy plants where significant increases in potentially beneficial fungi such as the basidiomycetes Ceratobasidium sp. and Mycena sp., the zygomycete Mortierella sp., and a member of Glomeralles were observed. However, the rhizosphere of diseased plants experienced a decrease in pathogenic basidiomycetes that can affect the root system, such as Thanatephorus cucumeris (the teleomorph of Rhizoctonia solani) and Calyptella sp.

Taxonomic and ecophysiological characteristics of actinobacteria in soils of the dry steppe zone of the Selenga Highlands (Western Transbaikalia)

Arid habitats have recently attracted increasing attention in terms of biodiversity research and the discovery of new bacterial species. These habitats are among the target ecosystems suitable for isolating new strains of actinobacteria that are likely to produce new metabolites. This paper presents the results on the isolation of actinobacteria from soils of the dry steppe zone of the Selenga Highlands, the characterization of their taxonomic diversity, as well as ecological and trophic properties. The bacterial counts on ISP 4 medium ranged from 6.6 × 105 to 7.1 × 106 CFU/g. The highest bacterial counts were observed in the subsurface and middle horizons of the studied soils. 28 strains of Gram-positive bacteria represented by thin-branched mycelium, coccoid and bacilliform forms were isolated. According to the results of 16S rRNA gene analysis, the isolated strains were representatives of Streptomyces, Arthrobacter, Glycomyces, Kocuria, Microbacterium, Micromonospora, Nocardioides, Pseudarthrobacter, and Rhodococcus (Actinomycetota). One isolate that showed low 16S rRNA gene sequence similarity with previously isolated and validly described species was a new species of the genus Glycomyces. It was shown that all tested strains are mesophilic, prefer neutral or slightly alkaline conditions, have growth limits in the temperature range of 5-45 °C and pH 6-9. The optimal NaCl concentration for growth of most strains was 0-1 %. The strains under study were capable of utilizing a wide range of mono- and disaccharides and polyatomic alcohols as a carbon source. The isolated strains were capable of using both organic (proteins and amino acids) and inorganic (ammonium salts and nitrates) compounds as nitrogen sources. The examinations of extracellular enzymes showed that all isolates were capable of producing catalase and amylase; 78.6 % of the total number of isolates produced protease and lipase; 53.6 %, cellulase; and 28.6 %, urease. The data obtained expand current knowledge about the diversity of microbial communities in soils of the Selenga Highlands and also confirm the potential of searching for new actinobacteria species in these soils.

Streptantibioticus silvisoli sp. nov., acidotolerant actinomycetes from pine litter, reclassification of Streptomyces cocklensis, Streptomyces ferralitis, Streptomyces parmotrematis and Streptomyces rubrisoli as Actinacidiphila cocklensis comb. nov., Streptantibioticus ferralitis comb. nov., Streptantibioticus parmotrematis comb. nov. and Streptantibioticus rubrisoli comb. nov., and emended descriptions of the genus Streptantibioticus, the family Streptomycetaceae and Streptomyces iconiensis

Filamentous actinomycetes, designated SL13 and SL54T, were isolated from pine litter and their taxonomic status resolved using a polyphasic approach. The isolates exhibit chemotaxonomic and morphological properties consistent with their classification in the family Streptomycetaceae. They form extensively branched substrate mycelia bearing aerial hyphae that differentiate into straight chains of cylindrical spores. The whole-organism hydrolysates contain ll-diaminopimelic acid, glucose, mannose and ribose, the predominant isoprenologue is MK-9(H8), the polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and glycophospholipids, and the major fatty acids are anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Phylogenetic trees based on 16S rRNA gene sequences and multilocus gene sequences of conserved housekeeping genes show that the isolates form a well-supported lineage that is most closely related to Streptomyces parmotrematis NBRC 115203T. All of these strains form a well-defined clade in the multilocus sequence analysis tree together with Streptantibioticus cattleyicolor DSM 46488T, Streptomyces ferralitis DSM 41836T and Streptomyces rubrisoli DSM 42083T. Draft genomes assemblies of the isolates are rich in biosynthetic gene clusters predicted to produce novel specialized metabolites and stress-related genes which provide an insight into how they have adapted to the harsh conditions that prevail in pine litter. Phylogenomically, both isolates belong to the same lineage as the type strains of S. cattleyicolor, S. ferralitis, S. parmotrematis and S. rubrisoli; these relationships are underpinned by high average amino acid identity, average nucleotide identity and genomic DNA-DNA hybridization values. These metrics confirm that isolates SL13 and SL54T belong to a novel species that is most closely related to S. parmotrematis NBRC 115203T and that these strains together with S. ferralitis DSM 41836T, S. rubrisoli DSM 42083T belong to the genus Streptantibioticus. Consequently, it is proposed that the isolates be recognized as a new Streptantibioticus species, Streptantibioticus silvisoli comb. nov., with isolate SL54T (=DSM 111111T=PCM3044T) as the type strain, and that S. ferralitis, S. parmotrematis and S. rubrisoli be transferred to the genus Streptantibioticus as Streptantibioticus ferralitis comb. nov., Streptantibioticus parmotrematis comb. nov. and Streptantibioticus rubrisoli comb. nov. Emended descriptions are given for the genus Streptantibioticus, the family Streptomycetaceae and for Streptomyces iconiensis which was found to be a close relative of the isolates in the 16S rRNA gene sequence analyses. It is also proposed that Streptomyces cocklensis be transferred to the genus Actinacidiphila as Actinacidiphila cocklensis comb. nov based on its position in the MLSA and phylogenomic trees and associated genomic data.

A panoramic view of the genomic landscape of the genus Streptomyces

We delineate the evolutionary plasticity of the ecologically and biotechnologically important genus Streptomyces, by analysing the genomes of 213 species. Streptomycetes genomes demonstrate high levels of internal homology, whereas the genome of their last common ancestor was already complex. Importantly, we identify the species-specific fingerprint proteins that characterize each species. Even among closely related species, we observed high interspecies variability of chromosomal protein-coding genes, species-level core genes, accessory genes and fingerprints. Notably, secondary metabolite biosynthetic gene clusters (smBGCs), carbohydrate-active enzymes (CAZymes) and protein-coding genes bearing the rare TTA codon demonstrate high intraspecies and interspecies variability, which emphasizes the need for strain-specific genomic mining. Highly conserved genes, such as those specifying genus-level core proteins, tend to occur in the central region of the chromosome, whereas those encoding proteins with evolutionarily volatile species-level fingerprints, smBGCs, CAZymes and TTA-codon-bearing genes are often found towards the ends of the linear chromosome. Thus, the chromosomal arms emerge as the part of the genome that is mainly responsible for rapid adaptation at the species and strain level. Finally, we observed a moderate, but statistically significant, correlation between the total number of CAZymes and three categories of smBGCs (siderophores, e-Polylysin and type III lanthipeptides) that are related to competition among bacteria.

Efficacy of Streptomyces murinus JKTJ-3 in Suppression of Pythium Damping-Off of Watermelon

Damping-off caused by Pythium aphanidermatum (Pa) is one of the most destructive diseases for watermelon seedlings. Application of biological control agents against Pa has attracted the attention of many researchers for a long time. In this study, the actinomycetous isolate JKTJ-3 with strong and broad-spectrum antifungal activity was screened from 23 bacterial isolates. Based on the morphological, cultural, physiological, and biochemical characteristics as well as the feature of 16S rDNA sequence, isolate JKTJ-3 was identified as Streptomyces murinus. We investigated the biocontrol efficacy of isolate JKTJ-3 and its metabolites. The results revealed that seed and substrate treatments with JKTJ-3 cultures showed a significant inhibitory effect on watermelon damping-off disease. Seed treatment with the JKTJ-3 cultural filtrates (CF) displayed higher control efficacy compared to the fermentation cultures (FC). Treatment of the seeding substrate with the wheat grain cultures (WGC) of JKTJ-3 exhibited better control efficacy than that of the seeding substrate with the JKTJ-3 CF. Moreover, the JKTJ-3 WGC showed the preventive effect on suppression of the disease, and the efficacy increased with increase in the inoculation interval between the WGC and Pa. Production of the antifungal metabolite actinomycin D by isolate JKTJ-3 and cell-wall-degrading enzymes such as β-1,3-glucanase and chitosanase were probably the mechanisms for effective control of watermelon damping-off. It was shown for the first time that S. murinus can produce anti-oomycete substances including chitinase and actinomycin D. This is the first report about S. murinus used as biocontrol agent against watermelon damping-off caused by Pa.

Biomineralization of pretilachlor by free and immobilized fungal strains isolated from paddy field

The excessive use of pretilachlor (a chloroacetamide herbicide) has raised concern throughout the world as it has been reported as highly toxic. The present study deals with isolating and screening pretilachlor degrading fungal strains. The strains Aspergillus ficuum (AJN2) and Aspergillus sp. (PDF1) isolated using enrichment technique were able to degrade 79% and 73% of pretilachlor respectively as analyzed using HPLC. Further, the immobilization technique was used in the study the pretilachlor degradation ability of the isolated strains. The immobilized spores of the strains AJN2 and PDF1 mineralized 84% and 95% of pretilachlor respectively. The degradation dynamics study revealed that the DT50 value of the herbicide was reduced to 2.4 d in aqueous medium due to the enhanced enzymatic activity. The enzymatic study showed high lignin peroxidase and manganese peroxidase activity by the strains AJN2 and PDF1 respectively. The study confirmed the efficient degradation of pretilachlor by Aspergillus ficuum (AJN2).

Recent Progress of Reclassification of the Genus Streptomyces

The genus Streptomyces is a representative group of actinomycetes and one of the largest taxa in bacteria, including approximately 700 species with validly published names. Since the classification was mainly based on phenotypic characteristics in old days, many members needed to be reclassified according to recent molecular-based taxonomies. Recent developments of molecular-based analysis methods and availability of whole genome sequences of type strains enables researchers to reclassify these phylogenetically complex members on a large scale. This review introduces reclassifications of the genus Streptomyces reported in the past decade. Appropriately 34 Streptomyces species were transferred to the other genera, such as Kitasatospora, Streptacidiphilus, Actinoalloteichus and recently proposed new genera. As a result of reclassifications of 14 subspecies, the genus Streptomyces includes only four subspecies at present in practice. A total of 63 species were reclassified as later heterotypic synonyms of previously recognized species in 24 published reports. As strong relationships between species and the secondary metabolite-biosynthetic gene clusters become clarified, appropriate classifications of this genus will not only contribute to systematics, but also provide significant information when searching for useful bioactive substances.

Role of Alternative Elicitor Transporters in the Onset of Plant Host Colonization by Streptomyces scabiei 87-22

Plant colonization by Streptomyces scabiei, the main cause of common scab disease on root and tuber crops, is triggered by cello-oligosaccharides, cellotriose being the most efficient elicitor. The import of cello-oligosaccharides via the ATP-binding cassette (ABC) transporter CebEFG-MsiK induces the production of thaxtomin phytotoxins, the central virulence determinants of this species, as well as many other metabolites that compose the 'virulome' of S. scabiei. Homology searches revealed paralogues of the CebEFG proteins, encoded by the cebEFG2 cluster, while another ABC-type transporter, PitEFG, is encoded on the pathogenicity island (PAI). We investigated the gene expression of these candidate alternative elicitor importers in S. scabiei 87-22 upon cello-oligosaccharide supply by transcriptomic analysis, which revealed that cebEFG2 expression is highly activated by both cellobiose and cellotriose, while pitEFG expression was barely induced. Accordingly, deletion of pitE had no impact on virulence and thaxtomin production under the conditions tested, while the deletion of cebEFG2 reduced virulence and thaxtomin production, though not as strong as the mutants of the main cello-oligosaccharide transporter cebEFG1. Our results thus suggest that both ceb clusters participate, at different levels, in importing the virulence elicitors, while PitEFG plays no role in this process under the conditions tested. Interestingly, under more complex culture conditions, the addition of cellobiose restored thaxtomin production when both ceb clusters were disabled, suggesting the existence of an additional mechanism that is involved in sensing or importing the elicitor of the onset of the pathogenic lifestyle of S. scabiei.

Generation of a high quality library of bioactive filamentous actinomycetes from extreme biomes using a culture-based bioprospecting strategy

Introduction

Filamentous actinomycetes, notably members of the genus Streptomyces, remain a rich source of new specialized metabolites, especially antibiotics. In addition, they are also a valuable source of anticancer and biocontrol agents, biofertilizers, enzymes, immunosuppressive drugs and other biologically active compounds. The new natural products needed for such purposes are now being sought from extreme habitats where harsh environmental conditions select for novel strains with distinctive features, notably an ability to produce specialized metabolites of biotechnological value.

Methods

A culture-based bioprospecting strategy was used to isolate and screen filamentous actinomycetes from three poorly studied extreme biomes. Actinomycetes representing different colony types growing on selective media inoculated with environmental suspensions prepared from high-altitude, hyper-arid Atacama Desert soils, a saline soil from India and from a Polish pine forest soil were assigned to taxonomically predictive groups based on characteristic pigments formed on oatmeal agar. One hundred and fifteen representatives of the colour-groups were identified based on 16S rRNA gene sequences to determine whether they belonged to validly named or to putatively novel species. The antimicrobial activity of these isolates was determined using a standard plate assay. They were also tested for their capacity to produce hydrolytic enzymes and compounds known to promote plant growth while representative strains from the pine forest sites were examined to determine their ability to inhibit the growth of fungal and oomycete plant pathogens.

Results

Comparative 16S rRNA gene sequencing analyses on isolates representing the colour-groups and their immediate phylogenetic neighbours showed that most belonged to either rare or novel species that belong to twelve genera. Representative isolates from the three extreme biomes showed different patterns of taxonomic diversity and characteristic bioactivity profiles. Many of the isolates produced bioactive compounds that inhibited the growth of one or more strains from a panel of nine wild strains in standard antimicrobial assays and are known to promote plant growth. Actinomycetes from the litter and mineral horizons of the pine forest, including acidotolerant and acidophilic strains belonging to the genera Actinacidiphila, Streptacidiphilus and Streptomyces, showed a remarkable ability to inhibit the growth of diverse fungal and oomycete plant pathogens.

Discussion

It can be concluded that selective isolation and characterization of dereplicated filamentous actinomyctes from several extreme biomes is a practical way of generating high quality actinomycete strain libraries for agricultural, industrial and medical biotechnology.

Draft genome sequence of Streptomyces sp. KD18, isolated from industrial soil

The present study scrutinizes the presence of Streptomyces strains in the soil sample collected from industrial area of Bahadurgarh (Haryana) India. The morphological approach manifested the isolated strain belong to Streptomyces species and named as Streptomyces sp. KD18. Sequencing of Streptomyces sp. KD18 genome was performed by Illumina Nextseq500 platform. 65 contigs were generated via SPAdes v3.11.1 and harboured genome size of 7.2 Mb. AntiSMASH server revealed the presence of 25 biosynthetic gene clusters in KD18 genome where BGC of lipstatin was of more interest from industrial and pharmaceutical purpose. The draft genome sequence represented via ANI values claimed that the KD18 strain belongs to Streptomyces toxytricini and finally named as S. toxytricini KD18. The LC-MS analysis of the extracted metabolite confirmed the production of lipstatin. The genome sequence data have been deposited to NCBI under the accession number of GCA_014748315.1.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03453-3.

Polyenic Antibiotics and Other Antifungal Compounds Produced by Hemolytic Streptomyces Species

Streptomyces are of great interest in the pharmaceutical industry as they produce a plethora of secondary metabolites that act as antibacterial and antifungal agents. They may thrive on their own in the soil, or associate with other organisms, such as plants or invertebrates. Some soil-derived strains exhibit hemolytic properties when cultivated on blood agar, raising the question of whether hemolysis could be a virulence factor of the bacteria. In this work we examined hemolytic compound production in 23 β-hemolytic Streptomyces isolates; of these 12 were soil-derived, 10 were arthropod-associated, and 1 was plant-associated. An additional human-associated S. sp. TR1341 served as a control. Mass spectrometry analysis suggested synthesis of polyene molecules responsible for the hemolysis: candicidins, filipins, strevertene A, tetrafungin, and tetrin A, as well as four novel polyene compounds (denoted here as polyene A, B, C, and D) in individual liquid cultures or paired co-cultures. The non-polyene antifungal compounds actiphenol and surugamide A were also identified. The findings indicate that the ability of Streptomyces to produce cytolytic compounds (here manifested by hemolysis on blood agar) is an intrinsic feature of the bacteria in the soil environment and could even serve as a virulence factor when colonizing available host organisms. Additionally, a literature review of polyenes and non-polyene hemolytic metabolites produced by Streptomyces is presented.

Genomic and phylogenomic insights into the family Streptomycetaceae lead to the proposal of six novel genera

The family Streptomycetaceae is a large and diverse family within the phylum Actinomycetota . The members of the family are known for their ability to produce medically important secondary metabolites, notably antibiotics. In this study, 19 type strains showing low 16S rRNA gene similarity (<97.3 %) to other members of the family Streptomycetaceae were identified and their high genetic diversity was reflected in a phylogenomic analysis using conserved universal proteins. This analysis resulted in the identification of six distinct genus-level clades, with two separated from the genus Streptacidiphilus and four separated from the genus Streptomyces . Compared with members of the genera Streptacidiphilus and Streptomyces , average amino acid identity (AAI) analysis of the novel genera identified gave values within the range of 63.9–71.3 %, as has been previously observed for comparisons of related but distinct bacterial genera. The whole-genome phylogeny was reconstructed using PhyloPhlAn 3.0 based on an optimized subset of conserved universal proteins, the results of AAI and percentage of conserved proteins (POCP) analyses indicated that these phylogenetically distinct taxa may be assigned to six novel genera, namely Actinacidiphila gen. nov., Mangrovactinospora gen. nov., Peterkaempfera gen. nov., Phaeacidiphilus gen. nov., Streptantibioticus gen. nov. and Wenjunlia gen. nov.

Streptomyces solincola sp. nov., isolated from soil in Malaysia

A urease-producing Gram-stain-positive actinobacterium, designated strain T5^T, was isolated from a soil sample collected at a highway hillslope in Selangor, Malaysia. The strain was found to produce pale yellowish-pink aerial mycelia with smooth long chain spores and extensively branched light yellowish-pink substrate mycelia on oatmeal agar. Strain T5^T grew at 15-37 °C, pH 6-11, and tolerated up to 9 % (w/v) NaCl, with optimal growth occurring at 28 °C, pH 6-9 and without NaCl. The whole-cell sugar hydrolysate of strain T5^T contained galactose, glucose and ribose. The ll-diaminopimelic acid isomer was detected in the cell wall. Diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol were found to be the predominant polar lipids. The main fatty acids were anteiso-C_17 : 0, iso-C_16 : 0, anteiso-C_15 : 0 and iso-C_14 : 0. Comparative analysis of the 16S rRNA gene sequences indicated that strain T5^T belonged to Streptomyces of the family Streptomycetaceae with the highest 16S rRNA gene sequence similarity to Streptomyces lichenis LCR6-01^T (99.0 %). The overall genome relatedness indices revealed that the closest related species was S. lichenis LCR6-01^T with 89.4 % average nucleotide identity and 33.7 % digital DNA-DNA hybridization. Phylogeny analyses showed that strain T5^T was closely related to Streptomyces fradiae, Streptomyces lavendofoliae, Streptomyces lichenis, Streptomyces roseolilacinus and Streptomyces somaliensis. Based on these polyphasic data, strain T5^T represents a novel species, for which the name Streptomyces solincola sp. nov. is proposed. The type strain is T5^T (=TBRC 5137^T= DSM 42166^T).

Genome-based analyses reveal heterotypic synonyms of Streptomyces species and associated subspecies

In the genus Streptomyces, several validly described species have been reduced to synonyms of earlier described species though additional synonyms remain to be detected given the previous dependence on traditional phenotypic methods. In this study, genome-based procedures, including DNA-DNA hybridization analyses, overall genome-related indices, such as ANI, dDDH and AAI, revealed that certain strains recorded genomic indices above the threshold values used to define species boundaries. The results of phylogenetic and phylogenomic trees based on concatenated and phylogenomic analyses showed that 33 out of 364 tested species could be assigned to 15 species groups and that 18 Streptomyces species names be reclassified as later heterotypic synonyms of earlier validly published species. Consequently, it is proposed that S. albaduncus is a later heterotypic synonym of S. griseoloalbus; S. bellus is a synonym of S. coeruleorubidus; S. gancidicus and S. rubiginosus are synonyms of S. pseudogriseolus; S. niveoruber is a synonym of S. griseoviridis; S. griseomycini is a synonym of S. griseostramineus; S. jietaisiensis is a synonym of S. griseoaurantiacus; S. pluricolorescens is a synonym of S. rubiginosohelvolus; S. nashvillensis is a synonym of S. tanashiensis; S. yerevanensis is a synonym of S. flaveus; S. durhamensis is a synonym of S. filipinensis; S. recifensis is a synonym of S. griseoluteus; S. canaries and S. olivaceoviridis are synonyms of S. corchorusii; S. melanosporofaciens is a synonym of S. antimycoticus; S. albulus is a synonym of S. noursei; and S. janthinus and S. violarus are synonyms of S. violaceus. Additionally, seven of these 18 Streptomyces species have been designated subspecies.

Identification of Cyclic Dipeptides and a New Compound (6-(5-Hydroxy-6-methylheptyl)-5,6-dihydro-2H-pyran-2-one) Produced by Streptomyces fungicidicus against Alternaria solani

As an important microbial resource, Actinomycetes, especially Streptomyces, have important application values in medicine and biotechnology. Streptomyces fungicidicus SYH3 was isolated from soil samples in tomato-growing areas and showed good inhibitory effects on Alternaria solani in tomato. To obtain pure active compounds, SYH3 fermentation broth was subjected to XAD-16 macroporous resin and silica gel column chromatography. Combined with the repeated preparation and separation of preparative high-performance liquid chromatography (HPLC), a total of four monomer compounds were obtained after activity tracking. Compound 4 was identified as a new six-membered lactone ring compound named 6-(5-hydroxy-6-methylheptyl)-5,6-dihydro-2H-pyran-2-one by 1D and 2D nuclear magnetic resonance (NMR) data and mass spectrometry (MS). The other three active compounds belong to the cyclodipeptide, and their half maximal inhibitory concentration (IC₅₀) values against A. solani were 43.4, 42.9, and 30.6 μg/mL, respectively. Compound 4 significantly inhibited the spore germination and induced swollen and deformed local hyphae of A. solani with an IC₅₀ value of 24.9 μg/mL. Compound 4 also had broad-spectrum antifungal activity and had a good antifungal effect on the tested plant-pathogenic fungi. The modes of action of new compound (4) still require further investigation, representing a novel and effective anti-fungal agent for future application.

Environmental filtering dominated the antibiotic resistome assembly in river networks

River networks play important roles in dissemination of antibiotic resistance genes (ARGs). The occurrence, diversity, and abundance of ARGs in river networks have been widely investigated. However, the assembly processes that shaped ARGs profiles across space and time are largely unknown. Here, the dynamics of ARGs profiles in river networks (Taihu Basin) were revealed by high-throughput quantitative PCR followed by multiple statistical analyses to assess the underlying ecological processes. The results revealed clear variations for ARGs profiles across wet, normal, and dry seasons. Meanwhile, a significant negative correlation (p < 0.01) was observed between the similarity of ARGs profiles and geographic distance, indicating ARGs profiles exhibited distance-decay patterns. Null model analysis showed that ARGs profiles were mainly assembled via deterministic processes. Redundancy analysis followed by hierarchical partitioning revealed that environmental attributes (mainly pH and temperature) were the major factors affecting the dynamics of ARGs profiles. Together, these results indicated that environmental filtering was the dominant ecological process that shaped ARGs profiles. This study enhances our understanding how the antibiotic resistome is assembled in river networks and will be beneficial for the development of management strategies to control ARGs dissemination.

Evaluation and comparison of antibiotic susceptibility profiles of Streptomyces spp. from clinical specimens revealed common and region-dependent resistance patterns

Notwithstanding the fact that streptomycetes are overlooked in clinical laboratories, studies describing their occurrence in disease and potential pathogenicity are emerging. Information on their species diversity in clinical specimens, aetiology and appropriate therapeutic treatment is scarce. We identified and evaluated the antibiotic susceptibility profile of 84 Streptomyces clinical isolates from the Czech Republic. In the absence of appropriate disk diffusion (DD) breakpoints for antibiotic susceptibility testing (AST) of Streptomyces spp., we determined DD breakpoints by correlation with the broth microdilution method and by the distribution of zone diameters among isolates. Correlation accuracy was high for 9 antibiotics, leading to the establishment of the most valid DD breakpoints for Streptomyces antibiotic susceptibility evaluation so far. Clinical strains belonged to 17 different phylotypes dominated by a cluster of strains sharing the same percentage of 16S rRNA gene sequence identity with more than one species (S. albidoflavus group, S. hydrogenans, S. resistomycificus, S. griseochromogenes; 70% of isolates). AST results showed that Streptomyces exhibited intrinsic resistance to penicillin, general susceptibility to amikacin, gentamycin, vancomycin and linezolid, and high percentage of susceptibility to tetracyclines and clarithromycin. For the remaining antibiotics, AST showed inter- and intra-species variations when compared to available literature (erythromycin, trimethoprim-sulfamethoxazole), indicating a region-dependent rather than species-specific patterns.

Identification and Characterization of a Multifunctional Biocontrol Agent, Streptomyces griseorubiginosus LJS06, Against Cucumber Anthracnose

Twenty-eight bacterial strains isolated from Chinese herb extracts, beer fermentation waste, and raw oyster shells were evaluated for their efficacy in controlling cucumber anthracnose. Four bacterial strains, namely TG01, TG02, LJS06, and LJS08, were found to effectively reduce the mycelial growth of Colletotrichum orbiculare COC3 on PDA media. Spraying or drenching LJS06 spore suspension before inoculation significantly p < 0.05 reduced disease severity; thus, LJS06 was subject to further characterization. On the basis of the morphological, physiological, and biochemical characteristics and a multilocus sequence analysis of partial 16S rRNA, atpD, rpoB, and trpB genes, LJS06 was identified to be Streptomyces griseorubiginosus (Ryabova and Preobrazhenskaya) Pridham et al. Physiological and biochemical tests revealed that S. griseorubiginosus LJS06 can produce amylase, cellulase, chitinase, protease, siderophore, polyamines, and indole-3-acetic acid. Thus, a culture filtrate of LJS06 (specifically SL06) was formulated and evaluated for its efficacy against conidial germination, appressorium formation, and anthracnose management. Diluted SL06 was found to significantly (p < 0.05) inhibit conidial germination and appressorium formation, which can be attributed to impaired membrane integrity, accumulated reactive oxygen species (ROS), and impaired energy metabolism in the conidia. In addition, the spraying and drenching of diluted SL06 before inoculation consistently and significantly (p < 0.05) reduced anthracnose severity. These results jointly suggest that S. griseorubiginosus LJS06 can aid in the management of cucumber anthracnose by directly inhibiting conidial function and priming the plant defense system.

Paradigms of actinorhizal symbiosis under the regime of global climatic changes: New insights and perspectives

Nitrogen occurs as inert and inaccessible dinitrogen gaseous form (N₂ ) in the atmosphere. Biological nitrogen fixation is a chief process that makes this dinitrogen (N₂ ) accessible and bioavailable in the form of ammonium (NH₄ ⁺ ) ions. The key organisms to fix nitrogen are certain prokaryotes, called diazotrophs either in the free-living form or establishing significant mutual relationships with a variety of plants. On such examples is ~95-100 MY old incomparable symbiosis between dicotyledonous trees and a unique actinobacterial diazotroph in diverse ecosystems. In this association, the root of the certain dicotyledonous tree (~25 genera and 225 species) belonging to three different taxonomic orders, Fagales, Cucurbitales, and Rosales (FaCuRo) known as actinorhizal trees can host a diazotroph, Frankia of order Frankiales. Frankia is gram-positive, branched, filamentous, sporulating, and free-living soil actinobacterium. It resides in the specialized, multilobed, and coralloid organs (lateral roots but without caps), the root nodules of actinorhizal tress. This review aims to provide systematic information on the distribution and the phylogenetic diversity of hosts from FaCuRo and their micro-endosymbionts (Frankia spp.), colonization mechanisms, and signaling pathways. We also aim to provide details on developmental and physiological imperatives for gene regulation and functional genomics of symbiosis, phenomenal restoration ecology, influences of contemporary global climatic changes, and anthropogenic impacts on plant-Frankia interactions for the functioning of ecosystems and the biosphere.

Resolution of housekeeping gene sequences used in MLSA for the genus Streptomyces and reclassification of Streptomyces anthocyanicus and Streptomyces tricolor as heterotypic synonyms of Streptomyces violaceoruber

Although 16S rRNA gene sequences are conventionally analysed in bacterial systematics, their resolution is not sufficient for species identification. Multilocus sequence analysis (MLSA) is a powerful method for species identification as well as the elucidation of phylogenetic relationships in the genus Streptomyces . Gene sequences of atpD, gyrB, recA, rpoB and trpB are generally used in MLSA for Streptomyces species. This study aims to evaluate the sequence analysis of one gene instead of all five genes to be employed for species identification. The resolution of atpD gene sequences was not necessarily able to distinguish closely related species. In contrast, trpB gene sequence similarities correlated to the MLSA-based evolutionary distances, especially among closely related strains. A pairwise similarity of 97.9 % in trpB gene sequences was proposed as the threshold for species delineation based on the feasibility examined using strain pairs that shared >99.93 % pairwise 16S rRNA gene sequence similarities. Resequencing the five housekeeping genes followed by MLSA suggested that Streptomyces anthocyanicus and Streptomyces tricolor are synonyms of Streptomyces violaceoruber .

The Grapevine Microbiome to the Rescue: Implications for the Biocontrol of Trunk Diseases

Grapevine trunk diseases (GTDs) are one of the most devastating pathologies that threaten the survival and profitability of vineyards around the world. Progressive banning of chemical pesticides and their withdrawal from the market has increased interest in the development of effective biocontrol agents (BCAs) for GTD treatment. In recent years, considerable progress has been made regarding the characterization of the grapevine microbiome, including the aerial part microbiome (flowers, berries and leaves), the wood microbiome, the root environment and vineyard soil microbiomes. In this work, we review these advances especially in relation to the etiology and the understanding of the composition of microbial populations in plants affected by GTDs. We also discuss how the grapevine microbiome is becoming a source for the isolation and characterization of new, more promising BCAs that, in the near future, could become effective tools for controlling these pathologies.

Characterization of Streptomyces nymphaeiformis sp. nov., and its taxonomic relatedness to other polyhydroxybutyrate-degrading streptomycetes

A polyhydroxybutyrate (PHB)-degrading actinomycete, strain SFB5AT, was identified as a species of Streptomyces based on its membrane fatty acid profile and the presence of ll-diaminopimelic acid in the cell wall. It formed sporulating mycelia on most agar media, but flat or wrinkled, moist colonies on trypticase soy agar. Spores were smooth, cylindrical, and borne on long, straight to flexuous chains. It produced a light brown diffusible pigment, but not melanin. Comparison of genomic digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values indicated that strain SFB5AT was related to Streptomyces litmocidini JCM 4394T, Streptomyces vietnamensis GIMV4.0001T, Streptomyces nashvillensis JCM 4498T and Streptomyces tanashiensis JCM 4086T, plus 11 other species. However, the dDDH and ANI values were well below the species differentiation thresholds of <70 and <95 %, respectively; also, multilocus sequence analysis distances exceeded the species threshold of 0.007. Moreover, strain SFB5AT differed from the other species in pigmentation and its ability to catabolize arabinose. Strain SFB5AT and 11 of its 15 closest relatives degraded PHB and have genes for extracellular, short-chain-length denatured polyhydroxyalkanoate depolymerases. These enzymes from strain SFB5AT and its closest relatives had a type 1 catalytic domain structure, while those from other relatives had a type 2 structure, which differs from type one in the position of a consensus histidine in the active site. Thus, phenotypic and genotypic differences suggest that strain SFB5AT represents a new species of Streptomyces, for which we propose the name Streptomyces nymphaeiformis sp. nov. The type strain is SFB5AT (=NRRL B-65520T=DSM 112030T).

Nigericin and Geldanamycin Are Phytotoxic Specialized Metabolites Produced by the Plant Pathogen Streptomyces sp. 11-1-2

Plant pathogens use a variety of mechanisms, including the production of phytotoxic specialized metabolites, to establish an infection of host tissue. Although thaxtomin A is considered the key phytotoxin involved in the development of potato scab disease, there is increasing evidence that other phytotoxins can play a role in disease development in some instances.

Streptomyces chiangmaiensis SSUT88A mediated green synthesis of silver nanoparticles: characterization and evaluation of antibacterial action against clinical drug-resistant strains

This study involved the characterization of AgNPs synthesized from soil isolate Streptomyces sp. SSUT88A and their antimicrobial activities. The strain SSUT88A revealed 98.8% similarity of the 16s rRNA gene to Streptomyces chiangmaiensis TA4-1T. The AgNPs were synthesized by mixing either intracellular or extracellular cell-free supernatant of strain SSUT88A with AgNO3. The synthesized AgNPs from intracellular cell-free supernatant and extracellular cell-free supernatant were designated as IS-AgNPs and ES-AgNPs, respectively. The IS-AgNPs showed maximum absorbance of UV-vis spectra at 418 nm, while ES-AgNPs revealed maximum absorbance at 422 nm. The TEM observation of synthesized AgNPs revealed a spherical shape with an average diameter of 13.57 nm for IS-AgNPs and 30.47 nm for ES-AgNPs. The XRD and XANES spectrum profile of both synthesized AgNPs exhibited similar spectrum energy, which corresponded to AgNPs. The IS-AgNPs revealed antimicrobial activity against clinical isolate drug-resistant bacteria (Acinetobacter baumannii, Escherichia coli 8465, Klebsiella pneumoniae 1617, and Pseudomonas aeruginosa N90PS), while ES-AgNPs had no antimicrobial activity. When compared to commercial AgNPs, IS-AgNPs exhibited antibacterial efficacy against all clinical isolate bacteria including A. baumannii, one of the most threatening multi-drug resistant strains, while commercial AgNPs did not. Thus, IS-AgNPs has potential to be further developed as an antimicrobial agent against drug-resistant bacteria.

Streptomyces caniscabiei sp. nov., which causes potato common scab and is distributed across the world

Fourteen strains of Streptomyces isolated from scab lesions on potato are described as members of a novel species based on genetic distance, morphological observation and biochemical analyses. Morphological and biochemical characteristics of these strains are distinct from other described phytopathogenic species. Strain NE06-02DT has white aerial mycelium and grey, cylindrical, smooth spores on rectus-flexibilis spore chains. Members of this species group can utilize most of the International Streptomyces Project sugars, utilize melibiose and trehalose, produce melanin, grow on 6–7 % NaCl and pH 5–5.5 media, and are susceptible to oleandomycin (100 µg ml−1), streptomycin (20 µg ml−1) and penicillin G (30 µg ml−1). Though the 16S rRNA gene sequences from several members of this novel species are identical to the Streptomyces bottropensis 16S rRNA gene sequence, whole-genome average nucleotide identity and multi-locus sequence analysis confirm that the strains are members of a novel species. Strains belonging to this novel species have been isolated from the United States, Egypt and China with the earliest known members being isolated in 1961 from common scab lesions of potato in both California, USA, and Maine, USA. The name Streptomyces caniscabiei sp. nov. is proposed for strain NE06-02DT (=DSM111602T=ATCC TSD-236T) and the other members of this novel species group.

Combination of rhizosphere bacteria isolated from resistant potato plants for biocontrol of potato late blight

BACKGROUND

Potato late blight (PLB) caused by Phytophthora infestans is one of the most devastating plant diseases. The heavy use of chemical control agents is at odds with the development of sustainable and environmentally friendly agriculture practices. It is necessary to screen the antagonistic microorganisms of P. infestans and provide a new choice of PLB biocontrol.

RESULTS

In vitro, eight bacterial strains (A, B, C, D, E, F, G, H) isolated from the rhizosphere of resistant potato plants had a significant inhibitory effect on the mycelium growth of P. infestans, and the inhibition rate was 35.02-79.20%. These isolates were assigned to Streptomyces, Pseudomonas, Saccharothrix and Nocardiopsis by phylogenetic analysis of 16S rRNA genes. Their physiological and biochemical characteristics suggested that they can produce cellulase and catalase, which may help to inhibit the infection of P. infestans. In vivo, each strain significantly inhibited the infection of P. infestans after individual inoculation into potato tubers, and no strains posed a pathogenic threat to tubers. In the field environment, multibacterial treatment significantly reduced the disease index. Compared with the control, multibacterial and single H treatment significantly increased the microbial species and abundance of the potato rhizosphere and enriched potential beneficial bacteria such as Rhizobiaceae. Meanwhile, multi-bacterial and single H treatment significantly reduced the abundance of Enterobacteriaceae and Bacillaceae.

CONCLUSION

Our results provide some valuable native strains from the potato rhizosphere with the ability to inhibit P. infestans in vivo and in vitro, which may be a new option for PLB biocontrol. © 2021 Society of Chemical Industry.

Genomic Organization of Streptomyces flavotricini NGL1 and Streptomyces erythrochromogenes HMS4 Reveals Differential Plant Beneficial Attributes and Laccase Production Capabilities

The genus Streptomyces has been explored in industrial sectors due to its endurance to environmental stresses, the production of a plethora of biomolecules, the biological remediation of soils, and alleviating plant stresses. The whole genome of NGL1 and HMS4 was sequenced due to the specific laccase activity against 2,6-dimethoxyphenol (2,6-DMP) and differential plant beneficial attributes. The deduced genome of 8.85 Mbp and 7.73 Mbp in size with a G+C content of 72.03% and 72.3% was obtained for NGL1 and HMS4, respectively. A total of 8438 and 7322 protein coding genes, 155 (130 tRNA, 25 rRNA) and 145 tRNA (121 tRNA, 24 rRNA) coding genes were predicted in NGL1 and HMS4, respectively. The comparative genomics of NGL1 and HMS4 showed 185 and 162 genes encoding for carbohydrate-active enzymes, respectively. The genomic ability of these strains to encode carbohydrate-active enzymes, laccase, and diversity of BGCs, along with plant beneficial attributes to suppress the plant pathogens can be used for several industrial and agricultural applications.

Adaptation to Endophytic Lifestyle Through Genome Reduction by Kitasatospora sp. SUK42

Endophytic actinobacteria offer great potential as a source of novel bioactive compounds. In order to investigate the potential for the production of secondary metabolites by endophytes, we recovered a filamentous microorgansism from the tree Antidesma neurocarpum Miq. After phenotypic analysis and whole genome sequencing we demonstrated that this organism, SUK42 was a member of the actinobacterial genus Kitasatospora. This strain has a small genome in comparison with other type strains of this genus and has lost metabolic pathways associated with Stress Response, Nitrogen Metabolism and Secondary Metabolism. Despite this SUK42 can grow well in a laboratory environment and encodes a core genome that is consistent with other members of the genus. Finally, in contrast to other members of Kitasatospora, SUK42 encodes saccharide secondary metabolite biosynthetic gene clusters, one of which with similarity to the acarviostatin cluster, the product of which displays α-amylase inhibitory activity. As extracts of the host plant demonstrate this inhibitory activity, it suggests that the potential medicinal properties of A. neurocarpum Miq might be provided by the endophytic partner and illustrate the potential for exploitation of endophytes for clinical or industrial uses.

Major Streptomyces species associated with fissure scab of potato in South Africa including description of Streptomyces solaniscabiei sp. nov

Streptomyces species are the causal agents of several scab diseases on potato tubers. A new type of scab symptom, caused by Streptomyces species, was observed in South Africa from 2010 onwards. The disease was initially thought to be caused by a single Streptomyces species, however, subsequent isolations from similar symptoms on other potato tubers revealed diversity of the Streptomyces isolates. The objective of this study was to characterise these isolates in order to determine what are the major species involved in the disease. This was done by sequencing and phylogenetic analyses of the 16S rDNA as well as five housekeeping genes, investigation of growth on different culture media, standard phenotypic tests and scanning electron microscopy of culture morphology. The presence of the pathogenicity island (PAI) present in plant pathogenic Streptomyces species was also investigated. The genomes of eight isolates, selected from the three main clades identified, were sequenced and annotated to further clarify species boundaries. Three isolates of each of the three main clades were also inoculated onto susceptible potato cultivars in order to establish the pathogenicity of the species. The results of the phylogenetic and genome analyses revealed that there are three main species involved, namely, Streptomyces werraensis, Streptomyces pseudogriseolus and a novel Streptomyces species that is described here as Streptomyces solaniscabiei sp. nov., with strain FS70^T (= PPPPB BD 2226^T = LMG 32103^T) as the type strain. The glasshouse trial results showed that all three of the Streptomyces species are capable of producing fissure scab symptoms. None of the Streptomyces isolates from fissure scab contained the full PAI and the mechanism of disease initiation still needs to be determined. Genomic comparisons also indicated that S. gancidicus Suzuki 1957 (Approved Lists 1980) is a later heterotypic synonym of S. pseudogriseolus Okami and Umezawa 1955 (Approved Lists 1980).

Comparative Genomics Reveals a Remarkable Biosynthetic Potential of the Streptomyces Phylogenetic Lineage Associated with Rugose-Ornamented Spores

The genus Streptomyces is one of the richest sources of secondary metabolite biosynthetic gene clusters (BGCs). Sequencing of a large number of genomes has provided evidence that this well-known bacterial genus still harbors a large number of cryptic BGCs, and their metabolites are yet to be discovered. When taking a gene-first approach for new natural product discovery, BGC prioritization would be the most crucial step for the discovery of novel chemotypes. We hypothesized that strains with a greater number of BGCs would also contain a greater number of silent unique BGCs due to the presence of complex regulatory systems. Based on this hypothesis, we employed a comparative genomics approach to identify a specific Streptomyces phylogenetic lineage with the highest and yet-uncharacterized biosynthetic potential. A comparison of BGC abundance and genome size across 158 phylogenetically diverse Streptomyces type strains identified that members of the phylogenetic group characterized by the formation of rugose-ornamented spores possess the greatest number of BGCs (average, 50 BGCs) and also the largest genomes (average, 11.5 Mb). The study of genetic and biosynthetic diversities using comparative genomics of 11 sequenced genomes and a genetic similarity network analysis of BGCs suggested that members of this group carry a large number of unique BGCs, the majority of which are cryptic and not associated with any known natural product. We believe that members of this Streptomyces phylogenetic group possess a remarkable biosynthetic potential and thus would be a good target for a metabolite characterization study that could lead to the discovery of novel chemotypes.

IMPORTANCE It is now well recognized that members of the genus Streptomyces still harbor a large number of cryptic BGCs in their genomes, which are mostly silent under laboratory culture conditions. Activation of transcriptionally silent BGCs is technically challenging and thus forms a bottleneck when taking a gene-first approach for the discovery of new natural products. Thus, it is important to focus activation efforts on strains with BGCs that have the potential to produce novel metabolites. The clade-level analysis of biosynthetic diversity could provide insights into the relationship between phylogenetic lineage and biosynthetic diversity. By exploring BGC abundance in relation to Streptomyces phylogeny, we identified a specific monophyletic lineage associated with the highest BGC abundance. Then, using a combined analysis of comparative genomics and a genetic network, we demonstrated that members of this lineage are genetically and biosynthetically diverse, contain a large number of cryptic BGCs with novel genotypes, and thus would be a good target for metabolite characterization studies.

Biodiversity of Actinomycetes from Heavy Metal Contaminated Technosols

Technosols are artificial soils generated by diverse human activities and frequently contain toxic substances resulting from industrial processes. Due to lack of nutrients and extreme physico-chemical properties, they represent environments with limited bacterial colonization. Bacterial populations of technosols are dominated usually by Actinobacteria, including streptomycetes, known as a tremendous source of biotechnologically important molecules. In this study, the biodiversity of streptomycete-like isolates from several technosols, mainly mine soils and wastes (landfills and sludge) in Slovakia, was investigated. The combination of basic morphological and biochemical characterisations, including heavy metal resistance determination, and molecular approaches based on 16S rRNA gene analysis were used for the identification of the bacterial strains. From nine isolates of Actinobacteria collected from different habitats, one was found to represent a new species within the Crossiella genus. Eight other isolates were assigned to the genus Streptomyces, of which at least one could represent a new bacterial species. Some isolates showed high resistance to Pb, Zn, Cu or Ni. The most tolerated metal was Pb. The results obtained in this study indicate that technosols are a prospective source of new actinomycete species resistant to heavy metals what underlines their bioremediation potential.

Developing Actinobacterial Endophytes as Biocontrol Products for Fusarium pseudograminearum in Wheat

Crown rot of wheat, caused by Fusarium pseudograminearum, results in millions of dollars of yield losses globally each year. Management strategies to control crown rot are limited and there are concerns about development of fungicide resistance so novel treatment strategies are desirable. A collection of endophytic Actinobacteria was screened for their ability to suppress the growth of F. pseudograminearum and the development of crown rot symptoms in wheat with the aim of identifying candidates that can be developed into biocontrol products. The ability of the Actinobacteria isolates to suppress the growth of three different F. pseudograminearum strains in vitro was assessed using agar-plate competition assays. Soil-free seedling assays were used to screen for suppression of development of early disease symptoms in the susceptible wheat (Triticum aestivum) cv. Tamaroi. Four of the isolates were tested in a glasshouse pot experiment to assess their ability to decrease disease symptoms and prevent yield losses in wheat cv. Tamaroi grown to maturity in an unsterilized soil. The screening of 53 isolates identified two Streptomyces isolates, MH71 and MH243, with very strong antifungal activity against F. pseudograminearum strains in agar-plate competition and seedling assays. In the glasshouse pot trial, plants treated with seed coatings of either MH71 or MH243 had > 24% lower disease severity than control plants infected with F. pseudograminearum. These two cultures show potential for development as biocontrol products because they are easy to culture, grow on relatively inexpensive media, produce highly durable spores and can be delivered to plants as a seed coat.

Solid-Phase Extraction Embedded Dialysis (SPEED), an Innovative Procedure for the Investigation of Microbial Specialized Metabolites

Solid-phase extraction embedded dialysis (SPEED technology) is an innovative procedure developed to physically separate in-situ, during the cultivation, the mycelium of filament forming microorganisms, such as actinomycetes and fungi, and the XAD-16 resin used to trap the secreted specialized metabolites. SPEED consists of an external nylon cloth and an internal dialysis tube containing the XAD resin. The dialysis barrier selects the molecular weight of the trapped compounds, and prevents the aggregation of biomass or macromolecules on the XAD beads. The external nylon promotes the formation of a microbial biofilm, making SPEED a biofilm supported cultivation process. SPEED technology was applied to the marine Streptomyces albidoflavus 19-S21, isolated from a core of a submerged Kopara sampled at 20 m from the border of a saltwater pond. The chemical space of this strain was investigated effectively using a dereplication strategy based on molecular networking and in-depth chemical analysis. The results highlight the impact of culture support on the molecular profile of Streptomyces albidoflavus 19-S21 secondary metabolites.