Actinomycetes from Eucalyptus and their biological activities for controlling Eucalyptus leaf and shoot blight

Pseudonocardia spirodelae sp. nov., isolated from duckweed and formal proposal to reclassify Pseudonocardia antarctica as a later heterotypic synonym of Pseudonocardia alni and reclassify Pseudonocardia carboxydivorans as Pseudonocardia alni subsp. carboxydivorans

A novel Pseudonocardia strain DW16-2T, isolated from duckweed (Spirodela polyrhiza), was taxonomically studied in detail. The analysis based on its 16S rRNA gene sequence revealed that the strain was most closely related to Pseudonocardia carboxydivorans Y8T (98.8%), followed by Pseudonocardia tropica YIM 61452T (98.7%), Pseudonocardia antarctica DVS 5a1T (98.7%) and Pseudonocardia alni DSM 44104T (98.7%). The average nucleotide identity (ANI) based on blast and digital DNA-DNA hybridization (dDDH) relatedness values between strain DW16-2T and their closest type strains were below the threshold values for identifying a novel species. Morphological, physiological and chemotaxonomic features of strain DW16-2T were typical for the genus Pseudonocardia by forming extensively branched substrate mycelium and aerial mycelium that fragmented into rod-shaped spore, with a smooth surface. The whole-cell hydrolysates of strain DW16-2T contained meso-diaminopimelic acid as the diagnostic diamino acid, and the whole-cell sugars were arabinose, galactose, glucose and a trace amount of ribose. The polar lipids contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and unidentified phospholipids. The menaquinone (MK) was MK-8(H4). The cellular fatty acids (>5 %) were iso-C16 : 0, iso-C16 : 1 H, summed feature 3: C16 : 1 ω7c/C16 : 1 ω6c; C16 : 1 ω6c/C16 : 1 ω7c, C17 : 1 ω8c and anteiso-C17 : 0. Characterization based on chemotaxonomic, phenotypic, genotypic and phylogenetic evidence demonstrated that strain DW16-2T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia spirodelae sp. nov. (type strain DW16-2T = TBRC 16418T = NBRC 115857T) is proprosed. In addition, the comparison of the whole genome sequences suggested that P. alni and P. antarctica belong to the same species and P. carboxydivorans is a subspecies of P. alni. Therefore, it is proposed that P. antarctica Prabahar et al. 2004 is reclassified as a later heterotypic synonym of P. alni (Evtushenko et al. 1989) Warwick et al. 1994, and P. carboxydivorans Park et al. 2008 is proposed as a subspecies of P. alni (Evtushenko et al. 1989) Warwick et al. 1994.

Identification, fermentation optimization, and biocontrol efficacy of actinomycete YG-5 for the prevention of Alternaria leaf spot disease in star anise

Star anise (Illicium verum), a valuable spice tree, faces significant threats from fungal diseases, particularly Alternaria leaf spot. This study investigates the potential of a soil-derived actinomycete strain, YG-5, as a biocontrol agent against Alternaria tenuissima, the causative pathogen on Alternaria leaf spot in star anise. Through comprehensive morphology, physiology, biochemistry, and genetic analyses, we identified the isolate as Streptomyces sp. YG-5. The strain exhibited broad-spectrum antimicrobial activity against several plant pathogens, with inhibition rates ranging between 36.47 to 80.34%. We systematically optimized the fermentation conditions for YG-5, including medium composition and cultivation parameters. The optimized process resulted in an 89.56% inhibition rate against A. tenuissima, a 14.72% improvement over non-optimized conditions. Notably, the antimicrobial compounds produced by YG-5 demonstrated stability across various temperatures, pH levels, and UV irradiation. In vivo efficacy trials showed promising results, with YG-5 fermentation broth reducing Alternaria leaf spot incidence on star anise leaves by 56.95%. These findings suggest that Streptomyces sp. YG-5 holds significant potential as a biocontrol agent against Alternaria leaf spot in star anise cultivation, offering a sustainable approach to disease management in this valuable crop.

Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov., two novel actinobacteria isolated from mangrove sediments and leaves of halophyte Sesuvium portulacastrum in Thailand

A polyphasic approach was used to characterize two novel actinobacterial strains, designated PKS22-38T and LSe1-13T, which were isolated from mangrove soils and leaves of halophyte Sesuvium portulacastrum (L.), respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that they belonged to the genus Gordonia and were most closely related to three validly published species with similarities ranging from 98.6 to 98.1 %. The genomic DNA G+C contents of strains PKS22-38T and LSe1-13T were 67.3 and 67.2 mol%, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 93.3 and 54.9 %, respectively, revealing that they are independent species. Meanwhile, the ANI and dDDH values between the two novel strains and closely related type strains were below 80.5 and 24.0 %, respectively. Strains PKS22-38T and LSe1-13T contained C16 : 0, C18 : 1  ω9c and C18 : 0 10-methyl (TBSA) as the major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as the main phospholipids. The predominant menaquinone was MK-9(H2). Based on phenotypic, chemotaxonomic, phylogenetic and genomic data, strains PKS22-38T and LSe1-13T are considered to represent two novel species within the genus Gordonia, for which the names Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov. are proposed, with strain PKS22-38T (=TBRC 17540T=NBRC 116256T) and strain LSe1-13T (=TBRC 17706T=NBRC 116396T) as the type strains, respectively.

Actinomycetospora lemnae sp. nov., A Novel Actinobacterium Isolated from Lemna aequinoctialis Able to Enhance Duckweed Growth

Duckweed-associated actinobacteria are co-existing microbes that affect duckweed growth and adaptation. In this study, we aimed to report a novel actinobacterium species and explore its ability to enhance duckweed growth. Strain DW7H6T was isolated from duckweed, Lemna aequinoctialis. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that the strain was most closely related to Actinomycetospora straminea IY07-55T (99.0%), Actinomycetospora chibensis TT04-21T (98.9%), Actinomycetospora lutea TT00-04T (98.8%) and Actinomycetospora callitridis CAP 335T (98.4%). Chemotaxonomic and morphological characteristics of strain DW7H6T were consistent with members of the genus Actinomycetospora, while average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between the draft genomes of this strain and its closely related type strains were below the proposed threshold values used for species discrimination. Based on chemotaxonomic, phylogenetic, phenotypic, and genomic evidence obtained, we describe a novel Actinomycetospora species, for which the name Actinomycetospora lemnae sp. nov. is proposed. The type strain is DW7H6T (TBRC 15165T, NBRC 115294T). Additionally, the duckweed-associated actinobacterium strain DW7H6T was able to enhance duckweed growth when compared to the control, in which the number of fronds and biomass dry weight were increased by up to 1.4 and 1.3 fold, respectively. Moreover, several plant-associated gene features in the genome of strain DW7H6T potentially involved in plant-microbe interactions were identified.

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.

Streptomyces humicola sp. nov., a novel actinobacterium isolated from peat swamp forest soil in Thailand

A polyphasic approach was used to describe strain RB6PN25^T, an actinobacterium isolated from peat swamp forest soil in Rayong Province, Thailand. The strain was a Gram-stain-positive and filamentous bacterium that contained ll-diaminopimelic acid, mannose and ribose in whole-cell hydrolysates. MK-9(H₈) was the major menaquinone. The major fatty acids were iso-C_16 : 0, anteiso-C_15 : 0 and iso-C_15 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, two unidentified glycophospholipids, two unidentified aminolipids and an unidentified phospholipid. The 16S rRNA gene sequences analysis indicated that it was most closely related to Streptomyces rubrisoli DSM 42083^T (97.6 %) and Streptomyces palmae TBRC 1999^T (97.4 %). Strain RB6PN25^T exhibited low average nucleotide identity and digital DNA-DNA hybridization values with S. rubrisoli DSM 42083^T (78.6 %, 23.2 %) and S. palmae TBRC 1999^T (76.0 %, 22.6 %). The DNA G+C content of strain RB6PN25^T was 69.9%. The results of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses reveal that strain RB6PN25^T represents a novel species of the genus Streptomyces, for which the name Streptomyces humicola sp. nov. is proposed. The type strain is RB6PN25^T (=TBRC 14819^T=NBRC 115204^T).

Actinomycetospora soli sp. nov., isolated from the rhizosphere soil of Averrhoa carambola L

A novel actinobacterium, designated strain SF1T, was isolated from the rhizosphere soil of a star fruit plant (Averrhoa carambola L.) collected from Bangkok, Thailand, and its taxonomic position was evaluated. The strain showed morphological, chemotaxonomic and phylogenetic characteristics consistent with its classification in the genus Actinomycetospora . Strain SF1T was an aerobic, Gram-stain-positive and non-motile actinobacterium. Growth occurred at 15–35 °C, at pH 4.0–12.0 and in the presence of 0–10 % (w/v) NaCl. The 16S rRNA gene sequence of strain SF1T showed the highest similarity to Actinomycetospora chiangmaiensis YIM 0006T (99.5 %), Actinomycetospora corticicola 014-5T (98.8 %) and Actinomycetospora endophytica A-T 8314T (98.8 %). The genome sequencing revealed a genome size of 6.52 Mbp and a DNA G+C content of 74.0 %. In addition, the average nucleotide identity values between strain SF1T and reference strains, A. chiangmaiensis DSM 45062T, A. corticicola DSM 45772T and A. endophytica TBRC 5722T, were found to be 86.1, 86.5 and 79.7 %, respectively, and the level of digital DNA–DNA hybridization between them were 32.4, 32.4 and 23.3 %, respectively. The whole-cell hydrolysates of strain SF1T contained meso-diaminopimelic acid as the diagnostic diamino acid, with arabinose, galactose, glucose and ribose as whole-cell sugars. The predominant menaquinone was MK-8(H4). Major cellular fatty acids were iso-C16 : 0 and a summed feature consisting of C16 : 1 ω6c/C16 : 1 ω7c. Characterization based on chemotaxonomic, phylogenetic, phenotypic and genomic evidence demonstrated that strain SF1T represents a novel species of the genus Actinomycetospora , for which the name Actinomycetospora soli sp. nov. is proposed. The type strain is strain SF1T (=TBRC 15166T= NBRC 115295T).

Pseudonocardia terrae sp. nov., an actinobacterium isolated from rice rhizosphere soil in Thailand

A novel actinomycete, designated strain RS11V-5T, was isolated from rhizosphere soil of Oryza sativa L. collected from Roi Et Province, Thailand, and its taxonomic position was evaluated. Cells of strain RS11V-5T were Gram-stain-positive, aerobic, and non-motile. Whole-cell hydrolysates contained meso-diaminopimelic acid, arabinose, galactose, glucose and ribose. MK-8(H4) was detected as the predominant menaquinone of this strain. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylmethylethanolamine, hydroxy-phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminolipid and an unidentified glycolipid. The major fatty acids were iso-C16 : 0, C16 : 0 and C16 : 1 ω7c/C16 : 1 ω6c. Phylogenetic analyses based on the 16S rRNA gene sequences showed that strain RS11V-5T belonged to the genus Pseudonocardia and had high 16S rRNA sequence similarity of 99.3 % to Pseudonocardia kujensis KCTC 29062T and less than 98.4 % to other members of the genus Pseudonocardia . The DNA G+C content of the strain RS11V-5T was 73.3 mol%. Strain RS11V-5T showed 46.5 % digital DNA–DNA hybridization, 92.2 % orthologous average nucleotide identity (OrthoANI), 90.2 % ANI based on blast and 92.7 % ANI based on MUMmer to P. kujensis KCTC 29062T. Based its phenotypic, genotypic, phylogenetic and chemotaxonomic characteristics, strain RS11V-5T represents a novel species of the genus Pseudonocardia , for which the name Pseudonocardia terrae sp. nov. is proposed. The type strain is RS11V-5T (=TBRC 15286T=NBRC 115296T).

Kitasatospora humi sp. nov., isolated from a tropical peat swamp forest soil, and proposal for the reclassification of Kitasatospora psammotica as a later heterotypic synonym of Kitasatospora aureofaciens

A polyphasic approach was used to describe strain RB6PN24T, a novel actinobacterium isolated from peat swamp forest soil collected from Rayong province, Thailand. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus Kitasatospora and showed the highest sequence similarities to Kitasatospora kifunensis IFO 15206T (98.7 %) and Kitasatospora acidiphila MMS16-CNU292T (98.5 %). Strain RB6PN24T contained major amounts of meso-diaminopimelic acid, galactose, mannose and ribose in the whole-cell hydrolysates. MK-9(H6) and MK-9(H8) were the predominant menaquinones of the micro-organism. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, an unidentified lipid, four unidentified aminolipids and six unidentified phospholipids. Mycolic acids were not present. The major fatty acids were iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0, iso-C17:0, anteiso-C17 : 0 and C16 : 0. The draft genome size of strain RB6PN24T was 8.09 Mbp, with 72.1 mol% G+C content and predicted to contain at least 44 biosynthetic gene clusters encoding diverse secondary metabolites. Furthermore, the strain exhibited low average nucleotide identity and digital DNA–DNA hybridization values with K. acidiphila MMS16-CNU292T (89.1 %, 42.4 %) and K. kifunensis DSM 41654T (79.5 %, 25.5 %). The results of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses revealed that strain RB6PN24T represents a novel species of the genus Kitasatospora , for which the name Kitasatospora humi sp. nov. is proposed. The type strain is RB6PN24T (=TBRC 14818T=NBRC 115116T). In addition, the comparison of the whole genome sequences and phenotypic features suggested that Kitasatospora aureofaciens and Kitasatospora psammotica belong to the same species. Therefore, it is proposed that K. psammotica is reclassified as a later heterotypic synonym of K. aureofaciens .

Microbispora oryzae sp. nov., isolated from leaves of rice plant (Oryza sativa L.)

An endophytic actinomycete, designated strain RL4-1S^T, was isolated from surface-sterilized leaves of rice plant (Oryza sativa L.) collected from Buri Rum province, Thailand. Its taxonomic status was determined using a polyphasic approach. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the strain RL4-1S^T belongs to the genus Microbispora and is most closely related to Microbispora rosea subsp. rosea ATCC 12950^T (98.5%). The strain forms pairs of spores on short sporophores borne on the aerial mycelium. Polar lipid profile of strain RL4-1S^T is diphosphatidylglycerol, hydroxy-phosphatidylethanolamine, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides, ninhydrin-positive glycophospholipid, two unidentified phospholipids, an unidentified aminolipid, and an unidentified glycolipid. MK-9(H₄), MK-9(H₂), and MK-9 are major menaquinones of this organism. The predominant cellular fatty acids are iso-C_16:0, C_17:0 and C_16:0. Strain RL4-1S^T contains meso-diaminopimelic acid, glucose, madurose and ribose in whole-cell hydrolysates. The draft genome of strain RL4-1S^T consists of 7.46 Mbp and has a G + C content 71.2 mol%. Digital DNA-DNA hybridization and average nucleotide identity values between the genome sequence of strain RL4-1S^T with Microbispora rosea subsp. rosea ATCC 12950^T are 26.0% and 80.7%, respectively. Based on data of genotypic, phenotypic, phylogenetic and chemotaxonomic analysis, strain RL4-1S^T represents a novel species of the genus Microbispora, for which the name Microbispora oryzae sp. nov. is proposed. The type strain is RL4-1S^T (= TBRC 14817^T = NBRC 115115^T).

A Novel Antifungal Actinomycete Streptomyces sp. Strain H3-2 Effectively Controls Banana Fusarium Wilt

Banana Fusarium wilt disease caused by Fusarium oxyspoum f. sp. cubense (Foc) seriously threatens the banana industry. Foc tropical race 4 (Foc TR4) can infect almost all banana cultivars. Compared with traditional physical and chemical practices, biocontrol strategy using beneficial microbes is considered as an environmentally sound option to manage fungal disease. In this study, a strain, H3-2, isolated from a non-infected banana orchard, exhibited high antifungal activity against Foc TR4. According to its morphological, physiological, and biochemical characteristics, the strain H3-2 was identified as Streptomyces sp. and convinced by the polymorphic phylogenic analysis of 16S rRNA sequences. Extracts of the strain H3-2 suppressed the growth and spore germination of Foc TR4 in vitro by destroying cell membrane integrity and mycelial ultrastructure. Notably, the strain and its extracts showed broad-spectrum antifungal activity against the selected seven fungal phytopathogens. Fourteen chemical compounds in the extracts were identified by gas chromatography–mass spectrometer (GC-MS), primarily phenolic compounds. Additional pot inoculation experiment demonstrated that the fermentation broth of the strain H3-2 promoted the growth of banana seedlings by efficiently inhibiting the spread of banana Fusarium wilt disease. This study demonstrated the potential application of the novel Streptomyces sp. H3-2 for the management of banana Fusarium wilt.

Plant Growth-Promoting Rhizobacteria HN6 Induced the Change and Reorganization of Fusarium Microflora in the Rhizosphere of Banana Seedlings to Construct a Healthy Banana Microflora

Streptomyces aureoverticillatus HN6 was isolated in our previous study and effectively controlled banana Fusarium wilt. We explored the role of HN6 in constructing a healthy rhizosphere microflora of banana seedlings. The method of antibiotic resistance was used to determine the colonization ability of HN6. The effect of HN6 on the rhizosphere microbial communities was assessed using culture-dependent and high-throughput sequencing. The effect of HN6 on the infection process of the pathogen was evaluated using a pot experiment and confocal laser scanning microscopy. The results showed that HN6 could prevent pathogen infection; it increased the nutrient content and diversity of the bacterial community in the rhizosphere, promoted plant growth, and decreased the mycotoxin fusaric acid content and abundance of pathogens in the banana rhizosphere. Thus, HN6 decreased the relative abundance of Fusarium species, increased the diversity of fungi, and increased the relative abundance of bacteria in the rhizosphere. HN6 induced the change and reorganization of the microbial community dominated by Fusarium in the rhizosphere of banana seedlings, and it evolved into a community dominated that was not conducive to the occurrence of diseases, shaping the rhizosphere microflora and promoting the growth of banana.

Actinobacteria in natural products research: Progress and prospects

Actinobacteria are well-recognised biosynthetic factories that produce an extensive spectrum of secondary metabolites. Recent genomic insights seem to impact the exploitation of these metabolically versatile bacteria in several aspects. Notably, from the isolation of novel taxa to the discovery of new compounds, different approaches evolve at a steady pace. Here, we systematically discuss the enduring importance of Actinobacteria in the field of drug discovery, the current focus of isolation efforts targeting bioactive Actinobacteria from diverse sources, recent discoveries of novel compounds with different bioactivities, and the relative employment of different strategies in the search for novel compounds. Ultimately, we highlight notable progress that will have profound impacts on future quests for secondary metabolites of Actinobacteria.

Pseudonocardia acidicola sp. nov., a novel actinomycete isolated from peat swamp forest soil

A novel actinobacterium, designated strain K10HN5^T, was isolated from a peat soil sample collected from Kantulee peat swamp forest, Surat Thani Province, Thailand and its taxonomic position was determined using a polyphasic approach. Strain K10HN5^T contained meso-diaminopimelic acid, arabinose, galactose, glucose and ribose in its whole-cell hydrolysates. The predominant menaquinone was MK-8(H₄). The major fatty acids were iso-C_16 : 0, iso-C_15 : 0 and iso-C_16 : 1H. Mycolic acids were not present. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxyphosphatidylethanolamine, hydroxyphosphatidylmethylethanolamine and phosphatidylinositol. The 16S rRNA gene sequence analysis indicated that it was closely related to Pseudonocardia bannensis DSM 45300^T (97.9 %) and Pseudonocardia xinjiangensis JCM 11839^T (97.9 %). Strain K10HN5^T exhibited low average nucleotide identity and digital DNA-DNA hybridization values with P. bannensis DSM 45300^T (82.6, 28.7 %) and P. xinjiangensis JCM11839^T (76.3, 22.2 %). The DNA G+C content of strain K10HN5^T was 72.4 mol%. Based on polyphasic data, strain K10HN5^T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia acidicola sp. nov. is proposed. The type strain is K10HN5^T (=TBRC 10048^T=NBRC 113897^T).

A Newly Isolated Streptomyces sp. YYS-7 With a Broad-Spectrum Antifungal Activity Improves the Banana Plant Resistance to Fusarium oxysporum f. sp. cubense Tropical Race 4

Fusarium wilt of banana caused by Fusarium oxysporum f. sp. cubense (Foc) is one of the most destructive diseases, severely limiting the development of banana industry. Especially, Foc tropical race 4 (Foc TR4) can infect and destroy almost all banana cultivars. Until now, there is still a lack of an effective method for controlling fusarium wilt. A biocontrol strategy using Actinobacteria is considered as a promising method for management of disease and pest. In this study, 229 Actinobacteria were isolated from rhizosphere soil samples of a primitive ecological mountain. An actinobacterium strain marked with YYS-7 exhibited a high antifungal activity against Foc TR4. Combining the physiological and biochemical characteristics as well as alignment of the 16S rRNA sequence, the strain YYS-7 was assigned to Streptomyces sp. The crude extracts of Streptomyces sp. YYS-7 obviously inhibited the mycelial growth of Foc TR4. The cell integrity and ultrastructure were seriously destroyed. In addition, Streptomyces sp. YYS-7 and crude extracts also showed a broad-spectrum antifungal activity against the selected seven phytopathogenic fungi. A gas chromatography-mass spectrometry (GC-MS) was used to predict the antifungal metabolites. A total of eleven different compounds were identified, including phenolic compounds, hydrocarbons, esters and acids. In the pot experiment, the crude extracts can significantly improve the banana plant’s resistance to Foc TR4. Hence, Streptomyces sp. YYS-7 will be a potential biocontrol agent for the biofertilizer exploitation and the discovery of new bioactive substances.

Description of the bacterial RNA polymerase inhibitor GE23077-producer Actinomadura sp. NRRL B-65521T as Actinomadura lepetitiana sp. nov

The filamentous actinomycete that produces the antibiotic GE23077 was isolated by the Lepetit Research Group from a soil sample collected in Thailand, and it was classified as a member of the genus Actinomadura on the basis of its morphology and cell-wall composition. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain formed a distinct monophyletic line within the genus Actinomadura, and it was most closely related to Actinomadura bangladeshensis DSM 45347^T (99.31 % similarity) and Actinomadura mexicana DSM 44485^T (98.94 %). The GE23077-producing strain formed an extensively branched, non-fragmented vegetative mycelium; no pseudosporangia were formed and the arthrospores were organized in slightly twisted chains. The cell wall contained meso-2,6-diaminopimelic acid and the diagnostic sugar was madurose. The predominant menaquinone was MK-9(H₆), with minor amounts of MK-9(H₈) and MK-9(H₄). The diagnostic phospholipids were phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were C_16 : 0 and tuberculostearic acid (10-methyloctadecanoic acid), followed by minor amounts of C_18:1ω9c, C_16:1ω7c and 10-methylheptadecanoic acid. The genomic DNA G+C content was 71.77 mol%. Significant differences in the morphological, chemotaxonomic and biochemical data, and the low DNA-DNA relatedness between the GE23077-producing strain and closely related type strains clearly demonstrate that it represents a novel species of the genus Actinomadura, for which the name Actinomadura lepetitiana sp. nov. is proposed. The type strain is NRRL B-65521^T(=LMG 31258^T=DSM 109019^T).

Biocontrol of chocolate spot disease (Botrytis cinerea) in faba bean using endophytic actinomycetes Streptomyces: a field study to compare application techniques

Sustainable agriculture is needing economic applications for disease control. One possibility is offered by local medical plants. Endophytes of medical plants, such as actinomycetes Streptomyces sp. have previously shown antagonistic activities against fungal phytopathogens. In the present field experiment, we aimed to verify the efficiency of endophytic Streptomyces against one of the common pathogens, Botrytis cinerea, causing chocolate spot disease for faba bean (Vicia fabae L.). We tested two strains of Streptomyces (MG788011, MG788012) and three techniques to apply the biocontrol agent: (1) coating the seeds with spores, (2) spraying mycelia and (3) spraying the crude metabolites over the plants. The technique using the crude metabolites was the most efficient to prevent the disease symptoms. Both of the endophytic strains diminished the disease symptoms and improved the plant growth. The study offers a potential biological control technique to prevent chocolate spot disease and, at the same time, increase the yields of faba bean in sustainable agriculture.

A novel strain of endophytic Streptomyces for the biocontrol of strawberry anthracnose caused by Glomerella cingulata

Anthracnose caused by Glomerella cingulata is one of the most devastating diseases of strawberry in Japan, particularly during its nursery period in the summer. In this study, we aimed to isolate and screen endophytic actinobacteria, to identify potential biocontrol agents capable of suppressing strawberry anthracnose. A total of 226 actinobacteria were successfully isolated from surface-sterilized strawberry tissues. In the first screening, 217 out of 226 actinobacteria isolates were studied for their suppression effect on strawberry anthracnose using a detached leaflet assay. It was discovered that isolates MBFA-172 and MBFA-227 markedly suppressed the development of anthracnose lesions. The efficacy of both isolates was then tested on two-month-old strawberry plug seedlings in a controlled environmental chamber. It was found that isolate MBFA-172 provided consistent disease suppression and was thus selected as a final candidate for further evaluation in a glasshouse experiment. Results showed that the severity as well as incidence rate of strawberry anthracnose was significantly reduced by treatment with isolate MBFA-172 compared with that of untreated control. Accordingly, the disease control efficacy provided by MBFA-172 was statistically comparable to the chemical fungicide propineb. A re-isolation experiment using a spontaneous thiostrepton-resistant mutated strain of isolate MBFA-172 revealed that it efficiently colonized the above-ground tissues of strawberry plants for at least three weeks after spray treatment. Using cultural, morphological, and physiological tests combined with 16S rRNA-based molecular analysis, MBFA-172 was identified as a moderately thermophilic Streptomyces thermocarboxydus-related species. Upon review, our results strongly indicated that MBFA-172 is a promising biocontrol agent for strawberry anthracnose.

Fermentation optimization and disease suppression ability of a Streptomyces ma. FS-4 from banana rhizosphere soil

Background

Fusarium wilt of banana is one of the most destructive diseases in banana-growing regions worldwide. Soil-borne diseases and soil microbial communities are closely related. The screening of antagonistic bacteria from soil microorganisms in areas with Fusarium wilt of banana is of great practical significance for controlling this disease.

Results

A strain designated FS-4 was isolated from healthy banana rhizosphere soil in an area affected by Fusarium wilt. This strain exhibited a significant antagonistic effect on the pathogen. Pot experiments revealed that the fermentation broth of strain FS-4 not only decreased the incidence of banana Fusarium wilt, but also promoted the growth of banana seedlings. The strain was identified as Streptomyces ma. by its morphological, physiological, and biochemical characteristics and 16S rRNA gene sequence analysis. The culture and fermentation conditions for this strain were optimized by single-factor and response surface experiments. The optimum culture conditions for Streptomyces ma. FS-4 were as follows: peptone 0.5%, saccharose 2.4, 0.05% K₂HPO₄, 0.05% MgCl₂, and 0.05% NaCl at an initial pH of 7.0; 180 g at 28 °C; and inoculation size of 6% for 62 h. The diameter of bacteriostasis circle for Bacillus subtilis reached 26.7 mm.

Conclusion

Streptomyces ma. FS-4 is an important microbial resource as a biological agent for the control of plant pathogenic fungi and can be used to promote banana growth.

Plant Microbiome and Its Link to Plant Health: Host Species, Organs and Pseudomonas syringae pv. actinidiae Infection Shaping Bacterial Phyllosphere Communities of Kiwifruit Plants

Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of the bacterial canker, the most devastating disease of kiwifruit vines. Before entering the host tissues, this pathogen has an epiphytic growth phase on kiwifruit flowers and leaves, thus the ecological interactions within epiphytic bacterial community may greatly influence the onset of the infection process. The bacterial community associated to the two most important cultivated kiwifruit species, Actinidia chinensis and Actinidia deliciosa, was described both on flowers and leaves using Illumina massive parallel sequencing of the V3 and V4 variable regions of the 16S rRNA gene. In addition, the effect of plant infection by Psa on the epiphytic bacterial community structure and biodiversity was investigated. Psa infection affected the phyllosphere microbiome structures in both species, however, its impact was more pronounced on A. deliciosa leaves, where a drastic drop in microbial biodiversity was observed. Furthermore, we also showed that Psa was always present in syndemic association with Pseudomonas syringae pv. syringae and Pseudomonas viridiflava, two other kiwifruit pathogens, suggesting the establishment of a pathogenic consortium leading to a higher pathogenesis capacity. Finally, the analyses of the dynamics of bacterial populations provided useful information for the screening and selection of potential biocontrol agents against Psa.

Growth Promotion and Disease Suppression Ability of a Streptomyces sp. CB-75 from Banana Rhizosphere Soil

An actinomycete strain, CB-75, was isolated from the soil of a diseased banana plantation in Hainan, China. Based on phenotypic and molecular characteristics, and 99.93% sequence similarity with Streptomyces spectabilis NBRC 13424 (AB184393), the strain was identified as Streptomyces sp. This strain exhibited broad-spectrum antifungal activity against 11 plant pathogenic fungi. Type I polyketide synthase (PKS-I) and non-ribosomal peptide synthetase (NRPS) were detected, which were indicative of the antifungal compounds that Streptomyces sp. CB-75 could produce. An ethyl acetate extract from the strain exhibited the lowest minimum inhibitory concentration (MIC) against Colletotrichum musae (ATCC 96167) (0.78 μg/ml) and yielded the highest antifungal activity against Colletotrichum gloeosporioides (ATCC 16330) (50.0 μg/ml). Also, spore germination was significantly inhibited by the crude extract. After treatment with the crude extract of Streptomyces sp. CB-75 at the concentration 2 × MIC, the pathogenic fungi showed deformation, shrinkage, collapse, and tortuosity when observed by scanning electron microscopy (SEM). By gas chromatography-mass spectrometry (GC-MS) of the crude extract, 18 chemical constituents were identified; (Z)-13-docosenamide was the major constituent. Pot experiments showed that the incidence of banana seedlings was reduced after using Streptomyces sp. CB-75 treatment. The disease index was 10.23, and the prevention and control effect was 83.12%. Furthermore, Streptomyces sp. CB-75 had a growth-promoting effect on banana plants. The chlorophyll content showed 88.24% improvement, the leaf area, root length, root diameter, plant height, and stem showed 88.24, 90.49, 136.17, 61.78, and 50.98% improvement, respectively, and the shoot fresh weight, root fresh weight, shoot dry weight, and root dry weight showed 82.38, 72.01, 195.33, and 113.33% improvement, respectively, compared with treatment of fermentation broth without Streptomyces sp. CB-75. Thus, Streptomyces sp. CB-75 is an important microbial resource as a biological control against plant pathogenic fungi and for promoting banana growth.

Cryptosporangium eucalypti sp. nov., an actinomycete isolated from Eucalyptus camaldulensis roots

A novel actinomycete, designated strain EURKPP3H10T, was isolated from surface-sterilized roots of Eucalyptus camaldulensis Dehnh., collected from Kamphaengphet Silvicultural Research Station, Kamphaengphet province, Thailand. The taxonomic position of strain EURKPP3H10T was studied using a polyphasic approach. Phylogenetic evaluation based on 16S rRNA gene sequence analysis showed that strain EURKPP3H10T belongs to the genus Cryptosporangium, with the highest sequence similarity to Cryptosporangium cibodasense LIPI11-2-Ac046T (99.2 %). Colonies of strain EURKPP3H10T were orange yellow. Spherical sporangia with motile spores were observed. The strain contained meso-diaminopimelic acid and acofriose, arabinose, galactose, glucose, mannose, xylose and ribose in whole-cell hydrolysates. The predominant menaquinones were MK-9(H8) and MK-9(H6). The major fatty acids were iso-C16 : 0, C17 : 1ω8c, C18 : 1ω9c and C17 : 0. The polar lipids of the strain were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and unknown lipids. The DNA G+C content of the genomic DNA was 71.5 mol%. Based on comparative analysis of physiological, biochemical and chemotaxonomic data, including DNA-DNA hybridization, strain EURKPP3H10T represents a novel species of the genus Cryptosporangium, for which the name Cryptosporangium eucalypti sp. nov. is proposed. The type strain is EURKPP3H10T (=BCC 77605T=NBRC 111482T).