Actinomycetospora callitridis sp. nov., an endophytic actinobacterium isolated from the surface-sterilised root of an Australian native pine tree

Streptomyces mahasarakhamensis sp. nov., an Endophytic Actinobacterium Isolated from Jasmine Rice and its Potential as plant Growth Promoter

Two endophytic actinobacteria, strains MK5T and MK7, were isolated from the surface-sterilized root of Jasmine rice (Oryza sativa KDML 105). These strains were aerobic actinobacteria with a well-developed substrate and aerial mycelia that formed spiral spore chains. The type strains that shared the high 16S rRNA gene sequence similarity with both strains were Streptomyces naganishii NBRC 12892T (99.4%), "Streptomyces griseicoloratus" TRM S81-3T (99.2%), and Streptomyces spiralis NBRC 14215T (98.9%). Strains MK5T and MK7 are the same species sharing a digital DNA-DNA hybridization (dDDH) value of 95.3% and a 16S rRNA gene sequence similarity of 100%. Chemotaxonomic data confirmed the affiliation of strains MK5T and MK7 to the genus Streptomyces. Strains MK5T and MK7 contained MK-9(H4) as a major menaquinone; the whole-cell sugar of both strains was galactose and glucose. The strain MK5T shared 93.4% average nucleotide identity (ANI)-Blast, 95.5% ANI-MUMmer, 93% average amino acid identity, and 61.3% dDDH with S. spiralis NBRC 14215T. The polyphasic approach confirmed that strain MK5T represents a novel species, and the name Streptomyces mahasarakhamensis sp. nov. is proposed. The type strain is MK5T (= TBRC 17754 = NRRL B-65683). Genome mining, using an in silico approach and searching biosynthesis gene clusters of strains MK5T and MK7, revealed that the genomes contained genes encoding proteins relating to plant growth promotion, bioactive compounds, and beneficial enzymes. Strains MK5T and MK7 could produce indole acetic acid and solubilize phosphate in vitro.

Actinomycetospora termitidis sp. nov., an insect-derived actinomycete isolated from termite (Odontotermes formosanus)

Strain Odt1-22T, an insect-derived actinomycete was isolated from a termite (Odontotermes formosanus) that was collected from Chanthaburi province, Thailand. Strain Odt1-22T was aerobic, Gram-stain-positive, and produced bud-like spore chain on the substrate hypha. According to chemotaxonomic analysis, strain Odt1-22T contained meso-diaminopimelic acid in peptidoglycan and the whole-cell hydrolysates contained arabinose, galactose, glucose, and ribose. The major menaquinone was MK-8(H4). The diagnostic phospholipids were diphosphatidylglycerol, hydroxyphosphatidylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. Phylogenetic analysis based on 16 S rRNA gene sequence revealed that strain Odt1-22T was identified to the genus Actinomycetospora and showed high similarity values with A. chiangmaiensis DSM 45062 T (99.24%), A. soli SF1T (99.24%) and A. corticicola 014-5 T (98.17%). The genomic size of strain Odt1-22T was 6.6 Mbp with 73.8% G + C content and 6355 coding sequences (CDSs). The genomic analysis, strain Odt1-22T and closely related species A. chiangmaiensis DSM 45062 T, A. soli SF1T and A. corticicola DSM 45772 T displayed the values of average nucleotide identity-blast (ANIb) at 83.7-84.1% and MUMmer (ANIm) at 86.6-87.0%. Moreover, the results of digital DNA-DNA hybridization values between strain Odt1-22T and related Actinomycetospora species were 45.8-50.5% that lower than the threshold value of commonly used to delineate separated species level. On the basis of phenotypic, chemotaxonomic, and genotypic data, strain Odt1-22T represented a novel species within the genus Actinomycetospora, for which the name Actinomycetospora termitidis sp. nov. is proposed. The type strain of the species is Odt1-22T (= TBRC 16192 T = NBRC 115965 T).

Co-inoculation of the endophytes Bacillus thuringiensis CAPE95 and Paenibacillus polymyxa CAPE238 promotes Tropaeolum majus L. growth and enhances its root bacterial diversity

Tropaeolum majus L. is a versatile edible plant that is widely explored due to its medicinal properties and as a key element in intercropping systems. Its growth could be improved by the use of biofertilizers that can enhance nutrient uptake by the plant or provide tolerance to different abiotic and biotic stresses. In a previous study, 101 endophytes isolated from T. majus roots showed more than three plant growth-promoting (PGP) features in vitro, such as phosphate mineralization/solubilization, production of siderophores, antimicrobial substances and indole-related compounds, and presence of the nifH gene. To provide sustainable alternatives for biofertilization, the genomes of two promising endophytes-CAPE95 and CAPE238-were sequenced to uncover metabolic pathways related to biofertilization. Greenhouse experiments were conducted with 216 seeds and 60 seedlings, half co-inoculated with the endophytes (treatment) and half inoculated with 1X PBS (control), and the impact of the co-inoculation on the plant's bacteriome was accessed through 16S rRNA gene metabarcoding. The strains CAPE95 and CAPE238 were taxonomically assigned as Bacillus thuringiensis and Paenibacillus polymyxa, respectively. Metabolic pathways related to the enhancement of nutrient availability (nitrogen fixation, sulfate-sulfur assimilation), biosynthesis of phytohormones (indole-3-acetic acid precursors) and antimicrobial substances (bacilysin, paenibacillin) were found in their genomes. The in vivo experiments showed that treated seeds exhibited faster germination, with a 20.3% higher germination index than the control on the eleventh day of the experiment. Additionally, treated seedlings showed significantly higher plant height and leaf diameters (p < 0.05). The bacterial community of the treated plants was significantly different from that of the control plants (p < 0.001) and showed a higher richness and diversity of species (Chao and Shannon indexes, p < 0.001). A higher relative abundance of potential synergistic PGP bacteria was also shown in the bacteriome of the treated plants, such as Lysinibacillus and Geobacter. For the first time, co-inoculation of B. thuringiensis and P. polymyxa was shown to have great potential for application as a biofertilizer to T. majus plants. The bacterial consortium used here could also be explored in other plant species in the future.

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 phytophilus sp. nov., an endophytic actinobacterium with biosynthesis potential as an antibiotic producer

An endophytic actinobacterium, strain PIP175^T, was isolated from the root sample of a native apricot tree (Pittosporum angustifolium) growing on the Bedford Park campus of Flinders University, Adelaide, South Australia. This strain is a Gram stain-positive, aerobic actinobacterium with well-developed substrate mycelia. Aerial mycelia rarely produce spores and the spore chain is spiral. Strain PIP175^T showed the highest 16S rRNA gene sequence similarity to Streptomyces aculeolatus DSM 41644^T (99.4 %). Other closely related phylogenetic representatives include Streptomyces synnematoformans DSM 41902^T (98.3 %), Streptomyces albospinus NBRC 13846^T (97.6 %), Streptomyces cacaoi subsp. cacaoi NRRL B-1220^T (97.5 %) and Streptomyces ruber NBRC 14600^T (97.4 %). The major cellular fatty acid of this strain was iso-C_16 : 0 and the major menaquinone was MK-9(H₆). The whole-cell sugar contained galactose, glucose and mannose. Chemotaxonomic data confirmed that strain PIP175^T belonged to the genus Streptomyces. Digital DNA-DNA hybridization, average nucleotide identity based on blast and OrthoANIu results between strain PIP175^T and S. aculeolatus DSM 41644^T were 60.0, 94.1 and 94.9 %, respectively. Genotypic and phenotypic data and genome analysis results allowed the differentiation of strain PIP175^T from its closest species with validly published names. Strain PIP175^T showed good activity against methicillin-resistant Staphylococcus aureus 03120385. Genome mining of strain PIP175^T revealed biosynthetic genes encoding proteins relating to antibiotic production, plant growth promotion and biodegradation enzymes. The name proposed for the new species is Streptomyces phytophilus sp. nov. The type strain is PIP175^T (=DSM 103379^T=TBRC 6026^T).

Streptomyces spinosus sp. nov. and Streptomyces shenzhenensis subsp. oryzicola subsp. nov. endophytic actinobacteria isolated from Jasmine rice and their genome mining for potential as antibiotic producers and plant growth promoters

Two endophytic actinobacteria, strains SBTS01^T and W18L9^T, were isolated from leaf sheath and leaf tissue, respectively, of Jasmine rice (Oryza sativa KDML 105) grown in a rice paddy field in Roi Et Province, Thailand. A polyphasic taxonomic study showed that both strains belong to the genus Streptomyces; they are aerobic, forming well-developed substrate mycelia and aerial mycelia with long chains of spores. Strain SBTS01^T shares high 16S rRNA gene sequence similarity with Streptomyces rochei NRRL B-2410 ^T (99.0%) and Streptomyces naganishii NRRL ISP-5282 ^T (99.0%). Strain W18L9^T shares high 16S rRNA gene sequence similarity with Streptomyces shenzhenensis DSM 42034 ^T (99.7%). The genotypic and phenotypic properties of strains SBTS01^T and W18L9^T distinguish these two strains from the closely related species with validly published names. The genome analysis showed the dDDH, ANIb and ANIm values of the draft genome between strain SBTS01^T and its close neighbour in the phylogenomic tree, Streptomyces corchorusii DSM 40340^T to be 54.1, 92.6, and 94.3%, respectively; similarly for strain W18L9^T and the closely related species S. shenzhenensis DSM 42034 ^T values were 72.5, 95.1 and 97.0%. The name proposed for the new species represented by the type strain SBTS01^T is Streptomyces spinosus (= NRRL B-65636 ^T = TBRC 15052^T). The name proposed for the novel subspecies of strain W18L9^T is Streptomyces shenzhenensis subsp. oryzicola (= NRRL B-65635 ^T = TBRC 15051^T). Recognition of this subspecies also permits the description of Streptomyces shenzhenensis subsp. shenzhenensis. Strains SBTS01^T and W18L9^T can produce antibiotic against rice and human pathogens and showed plant growth promoting properties such as production of indole acetic acid, cytokinin, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, siderophores and cellulase. Genomic data mining of these two strains confirmed their potential as antibiotic producers and plant growth promoters. Their genomes contain multiple biosynthetic gene clusters including those for terpene, type 1, 2 and 3 polyketide synthase, Non-ribosomal peptide synthetase and lanthipeptides. Genes encoding plant growth promoting traits such; nitrogen fixation, ACC deaminase, siderophore production and stress-related adaption may have ecological significance.

Roots of the xerophyte Panicum turgidum host a cohort of ionizing-radiation-resistant biotechnologically-valuable bacteria

Bacterial communities associated with roots of Panicum turgidum, exposed to arid conditions, were investigated with a combination of cultural and metataxonomic approaches. Traditional culture-based techniques were used and 32 isolates from the irradiated roots were identified as belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria phyla. Four actinobacterial strains were shown to be ionizing-radiation (IR)-resistant: Microbacterium sp. PT8 (4.8 kGy (kGy)), Micrococcus sp. PT11 (4.4 kGy), Kocuria rhizophila PT10 (2.9 kGy) and Promicromonospora panici PT9^T (2.6 kGy), based on the D₁₀ dose necessary for a 90% reduction in colony forming units (CFU). Concerning the investigation of microbial communities in situ, metataxonomic analyses of the diversity of IR-resistant microorganisms associated with irradiated roots revealed a marked dominance of Actinobacteria (46.6%) and Proteobacteria (31.5%) compared to Bacteroidetes (4.6%) and Firmicutes (3.2%). Gamma irradiation not only changed the structure of bacterial communities, but also affected their functional properties. Comparative analyses of metabolic profiles indicated the induction of several pathways related to adaptation to oxidative stress in irradiated roots, such as DNA repair, secondary metabolites synthesis, reactive oxygen species (ROS)-mitigating enzymes, etc. P. turgidum is emblematic of desert-adapted plants. Until now, there is no other work that has focused on the microbial profile of irradiated roots of this xerophyte.

Pseudonocardia pini sp. nov., an endophytic actinobacterium isolated from roots of the pine tree Callitris preissii

A Gram-positive, aerobic, actinobacterial strain with rod-shaped spores, CAP47R^T, which was isolated from the surface-sterilized root of a native pine tree (Callitris preissii), grown in South Australia is described. The major cellular fatty acid of this strain was iso-H-C_16:1 and major menaquinone was MK-8(H₄). The diagnostic diamino acid in the cell-wall peptidoglycan was identified as meso-diaminopimelic acid. These chemotaxonomic data confirmed the affiliation of strain CAP47R^T to the genus Pseudonocardia. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this strain in the family Pseudonocardiaceae, being most closely related to Pseudonocardia xishanensis JCM 17906^T (98.8%), Pseudonocardia oroxyli DSM 44984^T (98.7%), Pseudonocardia thailandensis CMU-NKS-70^T (98.7%), and Pseudonocardia ailaonensis DSM 44979^T (97.9%). The results of the polyphasic study which contain genome comparisons of ANIb, ANIm, and digital DNA-DNA hybridization revealed the differentiation of strain CAP47R^T from the closest species with validated names. This strain represents a novel species and the name proposed for this microorganism is Pseudonocardia pini sp. nov., indicating the source of this actinobacterium from a pine tree. The type strain is CAP47R^T (= DSM 108967^T = NRRL B-65534^T). Genome mining revealed that this strain contained a variety of genes encoding enzymes that can degrade hazardous chemicals.

Streptomyces adelaidensis sp. nov., an actinobacterium isolated from the root of Callitris preissii with potential for plant growth-promoting properties

An endophytic actinobacterium, strain CAP261^T was isolated from the surface sterilized root of Callitris preissii (Australian native pine tree). As a result of a polyphasic taxonomy study, this strain was identified as a member of the genus Streptomyces. This strain was an aerobic actinobacterium with well-developed substrate mycelia with loop spore chains and the spore surfaces are verrucose. The closest phylogenetic members which shared the highest 16S rRNA gene sequences similarity was Streptomyces bottropensis ATCC 25435 ^T at 98.1%. Chemotaxonomic data including cell wall components, major menaquinones, and major fatty acids confirmed the affiliation of strain CAP261^T to the genus Streptomyces. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with genome comparison study, allowed the genotypic and phenotypic differentiation of strain CAP261^T and the closest species with validly published names. ANIb, ANIm and dDDH values of strain CAP261^T and S. bottropensis ATCC 25435 ^T were 86.7%, 89.2% and 33.9%, respectively. The name proposed for the new species is Streptomyces adelaidensis sp. nov. The type strain is CAP261^T (= DSM 42026 ^T = NRRL B-24814 ^T).

Micromonospora veneta sp. nov., an endophytic actinobacterium with potential for nitrogen fixation and for bioremediation

Strain CAP181^T, an endophytic actinobacterium, was isolated from a surface sterilized root sample of a native pine tree, Flinders University, Adelaide, South Australia. Chemotaxonomic data including cell wall components, major fatty acids, and major menaquinones confirmed the affiliation of strain CAP181^T to the genus Micromonospora. This strain was Gram stain positive with well-developed substrate mycelia to form a single spore with hairy surface. The phylogenetic tree showed that M. coerulea NBRC 13504 ^T is the closest phylogenetic neighbour, sharing 99.2% 16S rRNA gene similarity and the next closest neighbor is M. chaiyaphumensis DSM 45246 ^T (98.7%). Genome mining of this strain revealed genes encoding to enzymes relating to nitrogen fixation and bioremediation. Based on genotypic and phenotypic studies including DNA-DNA hybridization data, strain CAP181^T was different from any of the closely related species with valid names. The name proposed for the new species is Micromonospora veneta sp. nov. The type strain is CAP181^T (= DSM 109713 ^T = NRRL B-65535 ^T).

Genome mining and description of Streptomyces albidus sp. nov., an endophytic actinobacterium with antibacterial potential

An endophytic actinobacterium, strain CAP215^T was isolated from the root sample of a native pine tree (Callitris preissii), Adelaide, South Australia. This strain was a Gram stain-positive, aerobic actinobacterium with well-developed substrate mycelia. It produced spiral chains of spores. The closest phylogenetic members which shared the highest 16S rRNA gene sequence similarity were Streptomyces marinus DSM 41968^T, Streptomyces haliclonae DSM 41970^T and Streptomyces karpasiensis K413^T at 98.2%, 98.0% and 97.9%, respectively. The major cellular fatty acid of this strain was anteiso-C_15:0 and major menaquinone was MK-9(H₄). Polar lipids of strain CAP215^T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol dimannoside and two unknown glycolipids. Chemotaxonomic data confirmed strain CAP215^T belonged to the genus Streptomyces. Genome of strain CAP215^T was 6.65 Mb with 69.8% DNA G + C content and contains 5992 coding sequences (CDS). Biosynthesis Genes Clusters (BGCs) comprised post-translationally modified peptides (RiPPs) cluster, genes encoding enzyme relating to antibiotic production; actinorhodin, surfactin and tetracenomycin. Genome mining of this strain identified genes encoding proteins relating to plant growth promotion such as pyrophosphatase, ectoine synthase, superoxide dismutase and siderophore production; penibactin and desferrioxamine E. Genes encoding beneficial enzymes; amylase, β-xylosidase, chitinase, lipase and protease were detected. The genome of this strain contained genes encoding enzymes degrading xenobiotic compounds such as 2,4-dichlorophenol 6-monooxygenase, nitroreductase and epoxide hydrolase. Also, genes encoding squalene, hopene and betacarotenoid production were observed. Digital DNA-DNA (dDDH) hybridization, Average Nucleotide Identity BLAST (ANIb), ANI-MUMmer (ANIm) between strain CAP215^T and S. marinus DSM 41968^T were 25.4 %, 82% and 86.4%, respectively. The data on the genotypic and phenotypic characteristics and genome analysis recognized the differentiation of strain CAP215^T with the closest species with valid names. The name Streptomyces albidus sp. nov. was proposed for which the type strain is CAP215^T (= DSM 42025^T = NRRL B-24815^T).

Amycolatopsis pittospori sp. nov., an endophytic actinobacterium isolated from native apricot tree and genome mining revealed the biosynthesis potential as antibiotic producer and plant growth promoter

An endophytic actinobacterium, strain PIP199^T, was isolated from a root sample of a native apricot growing on the Bedford Park campus of Flinders University, Adelaide, South Australia. The result of a polyphasic study showed that this strain was identified as a new member of the genus Amycolatopsis. Strain PIP199^T is an aerobic actinobacterium with well-developed substrate mycelia and aerial mycelia that form short chains of spores. Amycolatopsis keratiniphila subsp. keratiniphila DSM 44409^T (99.7%), Amycolatopsis lurida DSM 43134^T (99.6%) and Amycolatopsis keratiniphila subsp. nogabecina DSM 44586^T (99.4%) shared the highest 16S rRNA gene sequence similarity. A. keratiniphila subsp. keratiniphila DSM 44409^T and A. lurida DSM 43134^T were the closest phylogenetic neighbors. Chemotaxonomic data including major fatty acids, cell wall components and major menaquinones confirmed the affiliation of strain PIP199^T to the genus Amycolatopsis. The phylogenetic analysis, physiological and biochemical studies and genomic study, allowed the genotypic and phenotypic differentiation of strain PIP199^T and the closely related species with valid names. ANIb and dDDH values when compared to Amycolatopsis keratiniphila subsp. keratiniphila DSM 44409^T were 87.3% and 36.4%, respectively. The name proposed for the new species is Amycolatopsis pittospori sp. nov. The type strain is PIP199^T (= NRRL B-65536^T = TBRC 10618^T).

Microbispora clausenae sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of a Thai medicinal plant, Clausena excavala Burm. f

An endophytic actinobacterium, strain CLES2T, was discovered from the surface-sterilized stem of a Thai medicinal plant, Clausena excavala Burm. f., collected from the Phujong-Nayoa National Park, Ubon Ratchathani Province, Thailand. The results of a polyphasic taxonomic study identified this strain as a member of the genus Microbispora and a Gram-stain-positive, aerobic actinobacterium. It had well-developed substrate mycelia, which were non-motile and possessed paired spores. A phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this strain in the family Streptosporangiaceae, being most closely related to Microbispora bryophytorum NEAU-TX2-2T (99.4 %), Microbispora camponoti 2C-HV3T (99.2 %), Microbispora catharanthi CR1-09T (99.2 %) and Microbispora amethystogenes JCM 3021T and Microbispora fusca NEAU-HEGS1-5T (both at 99.1 %). The major cellular fatty acid of this strain was iso-C16 : 0 and major menaquinone was MK-9(H4). The polar lipid profile of strain CLES2T contained diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol and phosphatidylinositol dimannosides. These chemotaxonomic data confirmed the affiliation of strain CLES2T to the genus Microbispora. The DNA G+C content of this strain was 70 mol%. Digital DNA-DNA hybridization and average nucleotide identity blast values between strain CLES2T and M. catharanthi CR1-09T were 62.4 and 94.0 %, respectively. The results of the polyphasic study allowed the genotypic and phenotypic differentiation of strain CLES2T from its closest species with valid names. The name proposed for the new species is Microbispora clausenae sp. nov. The type strain is CLES2T (=DSM 101759T=NRRL B-65340T).

Draft genome sequence of Promicromonospora panici sp. nov., a novel ionizing-radiation-resistant actinobacterium isolated from roots of the desert plant Panicum turgidum

A novel strain of the genus Promicromonospora, designated PT9^T, was recovered from irradiated roots of the xerophyte Panicum turgidum collected from the Ksar Ghilane oasis in southern Tunisia. Strain PT9^T is aerobic, non-spore-forming, Gram- positive actinomycete that produces branched hyphae and forms white to yellowish-white colonies. Chemotaxonomic features, including fatty acids, whole cell sugars and polar lipid profiles, support the assignment of PT9^T to the genus Promicromonospora. The genomic relatedness indexes based on DNA-DNA hybridization and average nucleotide identity values revealed a significant genomic divergence between strain PT9^T and all sequenced type strains of the taxon. Phylogenomic analysis showed that isolate PT9^T was most closely related to Promicromonospora soli CGMCC 4.7398^T. Phenotypic and phylogenomic analyses suggest that isolate PT9^T represents a novel species of the genus Promicromonospora, for which the name Promicromonospora panici sp. nov. is proposed. The type strain is PT9^T (LMG 31103^T = DSM 108613^T).The isolate PT9^T is an ionizing-radiation-resistant actinobacterium (D₁₀ value = 2.6 kGy), with resistance to desiccation and hydrogen peroxide. The complete genome sequence of PT9^T consists of 6,582,650 bps with 71.2% G+C content and 6291 protein-coding sequences. This genome will help to decipher the microbial genetic bases for ionizing-radiation resistance mechanisms including the response to oxidative stress.