Actinomadura monticuli sp. nov., isolated from Darangshi Oreum (a volcanic cone), and the reclassification of Actinomadura glauciflava Lu et al. 2003 as a later heterotypic synonym of Actinomadura luteofluorescens (Shinobu 1962) Preobrazhenskaya et al. 1975 (Approved Lists 1980)

Two mycelium-forming actinobacterial strains, designated as DLS-47 and DLS-62T, were isolated from volcanic ash collected from the surface of a rock on the peak of Darangshi Oreum (a volcanic cone) in Jeju, Republic of Korea, and their taxonomic positions were investigated by a polyphasic approach. Both of the isolates showed growth at 20-42 °C, pH 6.0-9.0 and 0-1% (w/v) NaCl. Furthermore, DLS-47 was found to grow at 45 °C, while strain DLS-62T grew at pH 10.0 and 3% (w/v) NaCl. The 16S rRNA gene-based phylogeny showed that both of the isolates belonged to the genus Actinomadura; strain DLS-47 was most closely related to Actinomadura chokoriensis DSM 45346T (100% sequence identity), while strain DLS-62T formed a tight cluster with Actinomadura bangladeshensis DSM 45347T (99.5% sequence similarity). Morphological and chemotaxonomic characteristics supported the affiliation of the two isolates to the genus Actinomadura. Phylogenomic analysis based on 92 core gene sequences showed that both of the isolates were most closely related to A. chokoriensis DSM 45346T. Strain DLS-47 shared 100% of orthologous average nucleotide identity and digital DNA-DNA hybridization values with A. chokoriensis DSM 45346T, while strain DLS-62T showed orthologous average nucleotide identity ≤89.8% and digital DNA-DNA hybridization values ≤39.4% with strain DLS-47 and members of the genus Actinomadura. The results of phenotypic assays and comparison of overall genomic relatedness indices support the conclusion that strain DLS-47 (= KACC 23347=DSM 116423) is a strain of A. chokoriensis, while strain DLS-62T (= KACC 23345T = DSM 116424T) represents a new species of the genus Actinomadura, for which the name Actinomadura monticuli sp. nov. is proposed. Also, Actinomadura glauciflava Lu et al. 2003 is reclassified as a later heterotypic synonym of Actinomadura luteofluorescens (Shinobu 1962) Preobrazhenskaya et al. 1975 (Approved Lists 1980) based on analysis of overall genomic relatedness indices and phenotypic similarity.

Identification and anti-bacterial property of endophytic actinobacteria from Thymes kotschyanus, Allium hooshidaryae, and Cerasus microcarpa

The arbitrary and overuses of antibiotics have resulted in the emergence of multidrug resistance bacteria which encounters human to a serious public health problem. Thus, there is an ever-increasing demand for discovery of novel effective antibiotics with new modes of function against resistant pathogens. Endophytic actinobacteria (EA) have currently been considered as one of the most prospective group of microorganisms for discovery of therapeutic agents. This study aimed to isolate EA from Thymes kotschyanus, Allium hooshidaryae, and Cerasus microcarpa plants and to evaluate their antibacterial properties. The healthy samples were collected, dissected and surface-sterilized before cultured on four different selection media at 28 °C. Nine EA were isolated and identified based on morphological and molecular properties, and scanning electron micrograph analyses. Based on phylogenetic analysis, they were taxonomically grouped into four families Streptomycetaceae, Nocardiaceae, Micromonosporaceae, and Pseudonocardiaceae. Their branched aerial mycelia produced chains of cylindrical or cube or oval shaped spores with smooth or rough surfaces. Four strains; IKBG03, IKBG05, IKBG13, and IKBG17 had less than 98.65% sequence similarity to their closely related strains, which constitute them as novel species/strains. Besides, three strains; IKBG05, IKBG13, and IKBG18 were reported as endophytes for the first time. Preliminary antibacterial activity conducted on the all isolates revealed potent antibacterial effects against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. All isolates strongly inhibited the growth of at least one of the tested pathogens. Our results reveals that the test plants are novel sources for isolating a diverse group of rare and common actinobacteria that could produce a wide range of novel biologically active natural products with antibacterial activity which have a great potential in pharmaceutical and biotechnological applications.

Actinomadura violacea sp. nov., a madurastatin A1-producing strain isolated from lichen in Thailand

An actinomycete strain, LCR2-06^T, isolated from a lichen sample on rock collected from Chiang Rai Province (Pong Phra Bat Waterfall), Thailand, was characterized using a polyphasic approach. The strain grew at 25-45 °C, pH 6-11 and on International Streptomyces Project 2 agar plate with 5 % (w/v) NaCl. It contained meso-diaminopimelic acid as the diamino acid in whole-cell hydrolysates. Rhamnose, ribose, xylose, madurose, glucose and galactose were detected as whole-cell sugar hydrolysates. Mycolic acids were absent. The N-acyl type of muramic acid was acetyl. The strain contained C_16 : 0, TBSA 10-methyl C_18 : 0 and 2-hydroxy C_16 : 0 as the predominant fatty acids and MK-9(H₆), MK-9(H₄) and MK-9(H₈) as the major menaquinones. The major polar lipids were diphosphatidylglycerol, phosphatidylinositol and unidentified phospholipid. The draft genome of strain LCR2-06^T was closely related to Actinomadura barringtoniae TBRC 7225^T (99.2 %), Actinomadura nitritigenes NBRC 15918^T (98.8 %), Actinomadura montaniterrae TISTR 2400^T (98.5 %) and Actinomadura physcomitrii JCM 33455^T (97.9 %). The draft genome of LCR2-06^T was 11.1 Mb with 10 588 coding sequences with an average G+C content of 72.7 mol%. Results of genomic analysis revealed that the ANIb and ANIm values between strain LCR2-06^T and A. montaniterrae TISTR 2400^T were 90.0 and 92.0 %, respectively. The digital DNA-DNA hybridization value was 43.9 % in comparison with the draft genome of A. montaniterrae TISTR 2400^T. The strain produced an antibacterial compound active against Bacillus subtilis ATCC 6633 and Kocuria rhizophila ATCC 9341. The results of taxonomic analysis suggested that strain LCR2-06^T represented a novel species of the genus Actinomadura for which the name Actinomadura violacea sp. nov. is proposed. The type strain is LCR2-06^T (=JCM 33065^T=KCTC 49547^T=NBRC 114810^T=LMG 32136^T=TISTR 2935^T).

Actinomadura litoris sp. nov., an actinobacterium isolated from sandy soil in Sanya

A novel actinobacterium, designated strain NEAU-AAG5^T, was isolated from sandy soil collected from Niuwang island in Sanya, Hainan Province, PR China. The taxonomic position of the strain was investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain NEAU-AAG5^T belongs to the genus Actinomadura and shared highest sequence similarity with Actinomadura macra NBRC 14102^T (98.8 %). Strain NEAU-AAG5^T grows at 20-40 °C (optimum, 28 °C), pH 6-10 (optimum, pH 7) and has NaCl tolerance of 0-3 %. The menaquinones were identified as MK-9(H₄) (4.2 %), MK-9(H₆) (49.2 %) and MK-9(H₈) (46.5 %). The major fatty acids were C_16 : 0 (31.4 %), 10-methyl C_18 : 0 (21.3 %) and C_18 : 1  ω9c (15.7 %). The polar lipids were diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositolmannoside, phosphatidylglycerol and phosphoglycolipid. The genomic DNA G+C content of strain NEAU-AAG5^T based on whole genome sequences was 72.8 mol%. Digital DNA-DNA hybridization between strain NEAU-AAG5^T and its closest phylogenetic neighbour, A. macra NBRC 14102^T, resulted in similarity value of 28.0 % (<70 %). Additionally, the average nucleotide identity was 84.2 % for A. macra NBRC 14102^T. On the basis of phenotypic, genotypic and phylogenetic data, strain NEAU-AAG5^T can be characterized to represent a novel species of the genus Actinomadura, for which the name Actinomadura litoris sp. nov. is proposed. The type strain is NEAU-AAG5^T (=JCM 33456^T=CCTCC AA 2019043^T).

Actinomadura decatromicini sp. nov., isolated from mountain soil in Thailand

A novel actinomycete strain CYP1-5T was isolated from the mountain soil sample collected from Chaiyaphum province, Thailand and its taxonomic position was clarified by using a polyphasic taxonomic approach. The chemotaxonomic properties of strain CYP1-5T were consistent within the genus Actinomadura. Cell-wall peptidoglycan of this strain contained meso-diaminopimelic acid. Galactose, madurose, and ribose were presented as the diagnostic sugars in whole-cell hydrolysates. The major menaquinone was MK-9(H6). Major cellular fatty acids were iso-C16:0 and C16:0. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, and phosphatidylinositol mannoside were observed as predominant phospholipids. Based on the results of phylogenetic analyses of 16S rRNA gene sequence, strain CYP1-5T was constituent with the genus Actinomadura and was closely related to Actinomadura syzygii GKU157T (99.5%) and Actinomadura chibensis IFM 10266T (= JCM 14158T) (98.2%). The draft genome size of strain CYP1-5T was 9.30 Mb with 72.2 mol% of G + C content. Strain CYP1-5T showed ANIb values of 94.9% with A. syzygii GKU157T and 93.2% with A. chibensis JCM 14158T. Phenotypic characteristics, phylogenetic analysis and genome data support that strain CYP1-5T could be discriminated from its closest relatives, representing a novel species of the genus Actinomadura, for which the name Actinomadura decatromicini sp. nov. is proposed. The type strain is CYP1-5T (= JCM 16996T = KCTC 19916T = TISTR 2901T).

Actinomadura rubteroloni sp. nov. and Actinomadura macrotermitis sp. nov., isolated from the gut of the fungus growing-termite Macrotermes natalensis

The taxonomic positions of two novel aerobic, Gram-positive actinobacteria, designated strains RB29T and RB68T, were determined using a polyphasic approach. Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of RB29T were identified as Actinomadura rayongensis DSM 102126T (99.2 % similarity) and Actinomadura atramentaria DSM 43919T (98.7 %), and for strain RB68T was Actinomadura hibisca DSM 44148T (98.3 %). Digital DNA-DNA hybridization (dDDH) between RB29T and its closest phylogenetic neighbours, A. rayongensis DSM 102126T and A. atramentaria DSM 43919T, resulted in similarity values of 53.2 % (50.6-55.9 %) and 26.4 % (24.1-28.9 %), respectively. Additionally, the average nucleotide identity (ANI) was 93.2 % (94.0 %) for A. rayongensis DSM 102126T and 82.3 % (78.9 %) for A. atramentaria DSM 43919T. dDDH analysis between strain RB68T and A. hibisca DSM 44148T gave a similarity value of 24.5 % (22.2-27.0 %). Both strains, RB29T and RB68T, revealed morphological characteristics and chemotaxonomic features typical for the genus Actinomadura, such as the presence of meso-diaminopimelic acid in the cell wall, galactose and glucose as major sugar components within whole-cell hydrolysates and the absence of mycolic acids. The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. Predominant menaquinones were MK-9(H6) and MK-9(H8) for RB29T and MK-9(H4) and MK-9(H6) for RB68T. The main fatty acids were identified as 10-methyloctadecanoic acid (10-methyl C18:0), 14-methylpentadecanoic acid (iso-C16:0), hexadecanoic acid (C16:0) and cis-9-octadecanoic acid (C18 : 1 ω9c). Here, we propose two novel species of the genus Actinomadura: Actinomadura rubteroloni sp. nov. with the type strain RB29T (=CCUG 72668T=NRRL B-65537T) and Actinomadura macrotermitis sp. nov. with the type strain RB68T (=CCUG 72669T=NRRL B-65538T).

Actinomadura harenae sp. nov., a novel actinomycete isolated from sea sand in Sanya

A novel actinomycete, designated strain NEAU-Ht49^T, was isolated from sea sand sampled in Sanya and characterized by using a polyphasic approach. The 16S rRNA gene sequence analysis showed that strain NEAU-Ht49^T was most closely related to Actinomadura rhizosphaerae SDA37^T (98.8 %), Actinomadura logoneensis NEAU-G17^T (98.6 %), Actinomadura oligospora ATCC 43269^T (98.6 %) and Actinomadura gamaensis NEAU-Gz5^T (98.6 %). The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain NEAU-Ht49^T formed a cluster with A. rhizosphaerae SDA37^T, A. logoneensis NEAU-G17^T, A. oligospora ATCC 43269^T, A. gamaensis NEAU-Gz5^T and Actinomadura rupiterrae CS5-AC15^T (96.4 %). Meso-diaminopimelic acid was detected in its cell walls and glucose, madurose, mannose and ribose were detected in whole-cell hydrolysate. The polar lipids were found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositolmannoside and two unidentified lipids. The majoy menaquinone was MK-10(H₆) and the minor menaquinones were MK-9(H₄) and MK-9(H₈). The major fatty acids were C_16 : 0, C_18 : 1ω9c, 10-methyl C_18 : 0 and iso-C_16 : 0. Moreover, morphological and chemotaxonomic characteristics of properties of strain NEAU-Ht49^T also confirmed the affiliation of the isolate to the genus Actinomadura. However, DNA-DNA relatedness, physiological and biochemical data showed that strain NEAU-Ht49^T could be distinguished from its closest relatives. Therefore, strain NEAU-Ht49^T represents a novel species of the genus Actinomadura, for which the name Actinomadura harenae sp. nov. is proposed, with strain NEAU-Ht49^T (=CGMCC 4.7499^T=JCM 32659^T) as the type strain.

Actinomadura roseirufa sp. nov., producer of semduramicin, a polyether ionophore

The taxonomic position of 'Actinomadura roseorufa' LMG 30035^T, a semduramicin-producing mutant of strain ATCC 53666^P, which was isolated from a soil sample collected in Yamae Village, Kamamoto, Japan, was clarified in the present study using a polyphasic approach. This Gram-positive, aerobic actinomycete formed a well-developed, extensively branched, non-fragmenting substrate and aerial mycelia which differentiated into single, smooth-appearing spores. Based on analysis of nearly complete 16S rRNA gene sequence, strain LMG 30035^T was found to be closely related to the type strains of Actinomadura fibrosa ATCC 49459^T (98.88 %) and Actinomadura formosensis JCM 7474^T (98.82 %) (pairwise similarity values in parentheses). Digital DNA-DNA hybridisation experiments revealed unambiguously that strain LMG 30035^T represents a novel Actinomadura species (OrthoANIu values less than 83.1 %; dDDH values less than 27.2 % with type strains of validly named Actinomadura species). Analysis of the cell wall revealed the presence of meso-diaminopimelic acid in the peptidoglycan. The whole-cell sugars were glucose, madurose, galactose, ribose and rhamnose. The major polar lipids included phosphatidylinositol and diphosphatidylglycerol. The predominant menaquinones were MK-9(H₆), MK-9(H₈), MK-9(H₄) and MK-9(H₂). The major fatty acids were C_16 : 00, 10-methyl C_18 : 0, C_18 : 1  ω9c and C_18 : 00. The DNA G+C content of its genome was 72.5 mol%. In summary, these characteristics distinguish strain LMG 30035^T from validly named species of the genus Actinomadura, and therefore, we propose to classify this strain formally as the novel species Actinomadura roseirufa sp. nov. with LMG 30035^T (=CECT 9808^T,=ATCC 53664^T) as the type strain.

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

Actinomadura rhizosphaerae sp. nov., isolated from rhizosphere soil of the plant Azadirachta indica

A novel actinomycete, strain SDA37^T, belonging to the genus Actinomadura, was isolated from rhizosphere soil collected from Udon Thani Province, Thailand. The taxonomic position of the strain was characterized using a polyphasic approach. Meso-diaminopimelic acid, glucose, ribose, galactose and madurose were detected in cell-wall and whole-cell hydrolysates. The N-acyl type of muramic acid was acetyl. Menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The predominant cellular fatty acids were iso-C16 : 0, C16 : 0, 10-methyl C18 : 0 and iso-C14 : 0. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol. blast analysis of the almost-complete 16S rRNA gene sequence showed 98.8 % similarity to Actinomadura oligospora NBRC 104149^T, 98.7 % similarity to Actinomadura gamaensis DSM 100815^T and 97.2 % similarity to Actinomadura rupiterrae KCTC 19559^T. The DNA G+C content was 73.1 mol%. Strain SDA37^T showed low DNA-DNA relatedness (44.3±7.3 to 58.5±8.7 %) to A. oligospora NBRC 104149^T, Actinomadura gamaensis DSM 100815^T and Actinomadura rupiterrae KCTC 19559^T. The new strain could also be distinguished from its closely related strains by the differences in the phenotypic characteristics. The results of taxonomic analysis suggested that strain SDA37^T represented a novel species of the genus Actinomadura for which the name Actinomadura rhizosphaerae sp. nov. is proposed. The type strain is SDA37^T (=KCTC 39965^T=NBRC 112909^T=TISTR 2523^T).

Actinomadura barringtoniae sp. nov., an endophytic actinomycete isolated from the roots of Barringtonia acutangula (L.) Gaertn

A novel actinomycete strain, designated GKU 128^T, isolated from the roots of an Indian oak tree [Barringtonia acutangula (L.) Gaertn.] at Khao Khitchakut district, Chantaburi province, Thailand, was characterized by using a polyphasic approach. The strain formed a branched substrate and aerial mycelia which differentiated into straight to flexuous chains of smooth-ornamented spores. Analysis of the cell wall revealed the presence of meso-diaminopimelic acid and N-acetylmuramic acid in the peptidoglycan. The whole-cell sugars were glucose, madurose, mannose, rhamnose and ribose. Mycolic acids were absent. The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside. The predominant menaquinones were MK-9(H6), MK-9(H8), MK-9(H0) and MK-9(H4). The major fatty acids were C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0 (tuberculostearic acid). The genomic DNA G+C content was 70.5 mol%. Based on 16S rRNA gene sequence analysis, strain GKU 128^T was closely related to the type strains of Actinomadura nitritigenes NBRC 15918^T (99.2 % sequence similarity) and Actinomadura fibrosa JCM 9371^T (98.7 %). The levels of DNA-DNA relatedness between strain GKU 128^T and the closely related type species were less than 19 %. On the basis of phenotypic and genotypic characteristics, strain GKU 128^T could be distinguished from its closely related type strains and represents a novel species of the genus Actinomadura, for which the name Actinomadura barringtoniae sp. nov. (=TBRC 7225^T=NBRC 113074^T) is proposed.

Diversity and bioprospecting of actinomycete endophytes from the medicinal plants

The endophytic actinomycetes constitute one of the fascinating group of microorganisms associated with a wide range of plant species. The diversity of actinomycetes in plants and their tissue parts is a matter of debate as no consensus are derived between individual studies. Nevertheless, their diversity correlates with the occurrence in plant species harboured in unique regions of biologically diverse areas called "hot spots." Recent advances in the isolation techniques have facilitated the isolation of rare taxa from these environments. The biosynthetic ability of the endophytic actinomycetes has proven beyond doubt that these organisms have the potential to synthesize an array of compounds with novelty in structure and bioactivity and as a result are preferred in the natural product screening programs. In the years to come, the scientific world may await to discover many more novel actinomycete taxa with metabolic diversity and applications in therapeutics.

SIGNIFICANCE AND IMPACT OF THE STUDY

"Endophytes" - the microbes residing in the living tissues of plants are virtually omnipresent. Actinomycete endophytes are diverse in distribution within plant tissues, especially in the roots as they have a close association with the rhizhosphere. An introspection into diversity studies necessitates careful sampling, analysis, and isolation data from the biodiverse and nonbiodiverse regions represented by unique environments. The key to the recovery of novel species and their bioprospection lies in these regions.

Actinomadura alkaliterrae sp. nov., isolated from an alkaline soil

A polyphasic study was undertaken to establish the taxonomic status of an Actinomadura strain isolated from the margin of a saline, alkaline lake in Central Anatolia, Turkey. Strain D310AT^T was shown to have chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Actinomadura such as hooked or irregular spiral spore chains, meso-diaminopimelic acid as the major cell wall diaminopimelic acid, and diphosphatidylglycerol and phosphatidylinositol as major polar lipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain D310AT^T is closely, albeit loosely, associated with Actinomadura darangshiensis DLS-70^T with 97.2% sequence similarity, but was readily separated from the latter using diverse phenotypic properties. Consequently, the isolate is considered to represent a new species of Actinomadura for which the name Actinomadura alkaliterrae sp. nov. is proposed, with the type strain D310AT^T (=DSM 101185^T = KCTC 39657^T).

Actinomadura syzygii sp. nov., an endophytic actinomycete isolated from the roots of a jambolan plum tree (Syzygium cumini L. Skeels)

The taxonomic position of an endophytic actinomycete, strain GKU 157T, isolated from the roots of a jambolan plum tree (Syzygium cumini L. Skeels) collected at Khao Khitchakut National Park, Chantaburi province, Thailand, was determined using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis revealed that strain GKU 157T belongs to the genus Actinomadura and formed a distinct phyletic line with Actinomadura chibensis NBRC 106107T (98.6 % similarity). Strain GKU 157T formed an extensively branched, non-fragmenting substrate mycelium and aerial hyphae that differentiated into hooked to short spiral chains of about 20 non-motile spores with a warty surface. The cell wall contained meso-diaminopimelic acid and the whole-cell sugars were galactose, glucose, madurose, mannose and ribose. The N-acyl type of muramic acid was acetyl. Mycolic acids were absent. The phospholipids included phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylinositol (PI), phosphatidylinositolmannoside (PIM) and two unknown phospholipids (PLs). The major menaquinone was MK-9(H6) and the predominant fatty acids were C16:0, iso-C16:0, C18:1ω9c, C18:0 and 10-methyl C18:0 (tuberculostearic acid). The genomic DNA G+C content was 73.1 mol%. A combination of DNA–DNA hybridization results and significant differences from related species in cultural, physiological and chemical characteristics indicated that strain GKU 157T represents a novel species of the genus Actinomadura, for which the name Actinomadura syzygii sp. nov. is proposed. The type strain is GKU 157T ( = BCC 70456T = NBRC 110399T).

Biotechnological application and taxonomical distribution of plant growth promoting actinobacteria

Plant growth promoting (PGP) bacteria are involved in various interactions known to affect plant fitness and soil quality, thereby increasing the productivity of agriculture and stability of soil. Although the potential of actinobacteria in antibiotic production is well-investigated, their capacity to enhance plant growth is not fully surveyed. Due to the following justifications, PGP actinobacteria (PGPA) can be considered as a more promising taxonomical group of PGP bacteria: (1) high numbers of actinobacteria per gram of soil and their filamentous nature, (2) genome dedicated to the secondary metabolite production (~5 to 10 %) is distinctively more than that of other bacteria and (3) number of plant growth promoter genera reported from actinobacteria is 1.3 times higher than that of other bacteria. Mechanisms by which PGPA contribute to the plant growth by association are: (a) enhancing nutrients availability, (b) regulation of plant metabolism, (c) decreasing environmental stress, (d) control of phytopathogens and (e) improvement of soil texture. Taxonomical and chemical diversity of PGPA and their biotechnological application along with their associated challenges are summarized in this paper.

Actinomadura geliboluensis sp. nov., isolated from soil

A novel actinobacterium, strain A8036T, isolated from soil, was investigated by using a polyphasic taxonomic approach. The organism formed extensively branched substrate hyphae that generated spiral chains of spores with irregular surfaces. The cell wall contained meso-diaminopimelic acid (type III) and cell-wall sugars were glucose, madurose, mannose and ribose. The predominant menaquinones were MK-9(H6) and MK-9(H4). The phospholipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major cellular fatty acids were iso-C16 : 0, C17 : 1 cis9, C16 : 0, C15 : 0 and 10-methyl C17 : 0. Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain A8036T were Actinomadura meyerae DSM 44715T (99.23 % similarity), Actinomadura bangladeshensis DSM 45347T (98.9 %) and Actinomadura chokoriensis DSM 45346T (98.3 %). However, DNA–DNA relatedness and phenotypic data demonstrated that strain A8036T could be clearly distinguished from the type strains of all closely related Actinomadura species. Strain A8036T is therefore considered to represent a novel species of the genus Actinomadura , for which the name Actinomadura geliboluensis sp. nov. is proposed. The type strain is A8036T ( = DSM 45508T = KCTC 19868T).

Actinomadura rupiterrae sp. nov., isolated from cliff soil

A novel actinomycete strain, designated CS5-AC15T, was isolated from a soil sample collected from a cliff on Mara Island, Jeju, Republic of Korea, and subjected to a polyphasic taxonomic analysis. The isolate produced well-developed, yellow substrate mycelium and white aerial mycelium that differentiated into straight or flexuous chains of smooth-surfaced spores. 16S rRNA gene sequence analyses showed that the organism belonged to the family Thermomonosporaceae and formed a tight cluster with the type strain of Actinomadura oligospora (97.4 % sequence similarity). Chemotaxonomic characteristics were consistent with its assignment to the genus Actinomadura in that the isolate had meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall, madurose as the characteristic sugar, N-acetyl type of murein in the peptidoglycan, MK-9(H6) and MK-9(H8) as major menaquinones and a polar lipid profile containing diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unknown phospholipids. Mycolic acids were not detected. The predominant fatty acids were C16 : 0, C18 : 1ω9c and iso-C16 : 0. The DNA G+C content was 70.9 mol%. DNA relatedness of strain CS5-AC15T and A. oligospora JCM 10648T was 37.9±0.7 %. On the basis of the phenotypic, phylogenetic and DNA–DNA hybridization data, strain CS5-AC15T is assigned to a novel species of the genus Actinomadura, for which the name Actinomadura rupiterrae sp. nov. is proposed (type strain CS5-AC15T  = KCTC 19559T  = DSM 45251T).

Methods for the study of endophytic microorganisms from traditional Chinese medicine plants

Plant endophytes are very numerous and widely distributed in nature, their relationships being described as a balanced symbiotic continuum ranging from mutualism through commensalism to parasitism during a long period of coevolution. Traditional Chinese medicines have played a very important role in disease treatment in China and other Asian countries. Investigations show that these medicinal plants harbor endophytes with different kinds of ecological functions, and some of them have potential to produce bioactive small-molecule compounds. This chapter will focus on the selective isolation methods, the diversity of some endophytes (actinobacteria and fungi) isolated from Traditional Chinese Medicine (TCM) plants, and the bioactive compounds from selected endophytic actinobacteria reported in the past 3 years.

Actinomadura apis sp. nov., isolated from a honey bee (Apis mellifera) hive, and the reclassification of Actinomadura cremea subsp. rifamycini Gauze et al. 1987 as Actinomadura rifamycini (Gauze et al. 1987) sp. nov., comb. nov

A Gram-reaction-positive aerobic actinomycete, designated strain IM17-1(T), was isolated from a honey bee (Apis mellifera) hive in Chiang Mai Province, Thailand. The strain formed a branched substrate mycelium and mature aerial mycelium bore short chains of arthrospores with warty surfaces. The cell wall contained meso-2,6-diaminopimelic acid (cell-wall type III) and the whole cell sugars were fucose, galactose, glucose, madurose, mannose and ribose. The major isoprenoid quinone was hexahydrogenated menaquinone with nine isoprene units and the predominant cellular fatty acids were C₁₆:₀ (33.8 %), C₁₈:₁ω9c (32.7 %), summed feature 3 (C₁₆:₁ω7c and/or iso-C₁₅:₀ 2-OH) (8.7 %) and 10-methyl C₁₈:₀ (8.2 %). The phospholipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. These morphological and chemotaxonomic characteristics were consistent with the classification of IM17-1(T) within the genus Actinomadura. Based on 16S rRNA gene sequence analysis, strain IM17-1(T) was closely related to the type strains of Actinomadura cremea subsp. cremea (98.1 %) and Actinomadura cremea subsp. rifamycini (98.6 %); however, it represented a distinct phylogenetic lineage from the other species within this genus. The unique genetic characteristics were reaffirmed by low levels of DNA-DNA relatedness between strain IM17-1(T) and the two most closely related type strains, A. cremea subsp. cremea JCM 3308(T) (56.5±4.9 %) and A. cremea subsp. rifamycini JCM 3309(T) (31.0±22.6 %), and further supported the proposal of IM17-1(T) as a novel species. Strain IM17-1(T) ( = JCM 16576(T)  = TISTR 1980(T)) thus represents a novel species of the genus Actinomadura, for which the name Actinomadura apis sp. nov. is proposed. In addition, the genotypic and phenotypic data suggested the reclassification of Actinomadura cremea subsp. rifamycini Gauze et al. 1987 as a separate species, Actinomadura rifamycini sp. nov., comb. nov.

Bioprospecting microbial natural product libraries from the marine environment for drug discovery

Marine microorganisms are fascinating resources due to their production of novel natural products with antimicrobial activities. Increases in both the number of new chemical entities found and the substantiation of indigenous marine actinobacteria present a fundamental difficulty in the future discovery of novel antimicrobials, namely dereplication of those compounds already discovered. This review will share our experience on the taxonomic-based construction of a highly diversified and low redundant marine microbial natural product library for high-throughput antibiotic screening. We anticipate that libraries such as these can drive the drug discovery process now and in the future.