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

Diversity and antibacterial potential of the Actinobacteria associated with Apis mellifera ligustica

Insect-associated Actinobacteria are a potentially rich source of novel natural products with antibacterial activity. Here, the community composition of Actinobacteria associated with Apis mellifera ligustica was investigated by integrated culture-dependent and independent methods. A total of 61 strains of Streptomyces genera were isolated from the honeycomb, larva, and different anatomical parts of the honeybee's body using the culture-dependent method. Amplicon sequencing analyses revealed that the actinobacterial communities were dominated by the family of Bifidobacteriaceae and Microbacteriaceae in the honeybee gut, and Nocardiaceae and Pseudonocardiaceae in the honeycomb, whereas only Streptomyces genera were isolated by the culture-dependent method. Culture-independent analyses showed more diverse actinobacterial communities than those of culture-dependent methods. The antibacterial bioassay showed that most crude extracts of representative isolates exhibited antibacterial activities. Among them, the crude extract of Streptomyces sp. FCF01 showed the best antibacterial activities against Staphylococcus aureus, Micrococcus tetragenus, and Pseudomonas syringae pv. actinidiae (Psa) with the disc diameter of inhibition zone diameter (IZD) of 23.00, 15.00, and 13.33 mm, respectively. Chemical analysis of Streptomyces sp. FCF01 led to the isolation of three secondary metabolites, including mayamycin (1), mayamycin B (2), and N-(2-Hydroxyphenyl) acetamide (3). Among them, compound 1 displayed strong antibacterial activity against S. aureus, M. tetragenus, and Psa with minimum inhibitory concentrations (MIC) values of 6.25, 12.5, and 6.25 μg/ml, respectively. In addition, two novel derivative compounds 1a and 1b were synthesized by acetylation of compound 1. Both compounds 1a and 1b displayed similar antibacterial activities with those of metabolite 1. These results indicated that Streptomyces species associated with honeybees had great potential in finding antibiotics.

specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data

BACKGROUND

Understanding the factors that influence microbes' environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, "specificity" is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao's (Theor Popul Biol, 1982. https://doi.org/10.1016/0040-5809(82)90004-1, Sankhya A, 2010. https://doi.org/10.1007/s13171-010-0016-3 ) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables.

RESULTS

We present our R package specificity for performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well.

CONCLUSIONS

specificity is well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers using specificity's companion package, specificity.shiny.

Analysis of Major Bacteria and Diversity of Surface Soil to Discover Biomarkers Related to Soil Health

The discovery of biomarkers for assessing soil health requires the exploration of organisms that can explain the core functions of soil and identification of species with major roles in these functions. However, identifying specific keystone markers within the soil microbiota is challenging. Next-generation sequencing (NGS)-based molecular-biological methods have revealed information on soil biodiversity; however, whether this biodiversity is related to soil health remains unclear. In this study, we performed NGS on grassland surface soil to compare the prokaryotic and eukaryotic genetic diversity to determine the chemical soil quality and examined markers associated with soil health. Microorganisms associated with the nitrogen cycle, bioremediation, plant pathogenicity, antibiotic production, and material degradation showed potential for use as markers. To propose a framework for soil health assessment, we not only used traditional indicators, such as chemical and physical measures, but also assessed metagenomics data of soil by land use to identify the major factors influencing the microbial structure in soil. Moreover, major keystone species were identified. Furthermore, the microbial genetic diversity of generally healthy surface soil, such as forests, farmland, and parks, was determined. These findings provide basic data for exploring soil health-related biomarkers.

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).

Apis andreniformis associated Actinomycetes show antimicrobial activity against black rot pathogen (Xanthomonas campestris pv. campestris)

This study aimed to investigate cultivable actinomycetes associated with rare honey bee species in Thailand and their antagonistic activity against plant pathogenic bacteria. Actinomycetes were selectively isolated from the black dwarf honey bee (Apis andreniformis). A total of 64 actinomycete isolates were obtained with Streptomyces as the predominant genus (84.4%) followed by Micromonospora (7.8%), Nonomuraea (4.7%) and Actinomadura (3.1%). All isolates were screened for antimicrobial activity against Xanthomonas campestris pv. campestris, Pectobacterium carotovorum and Pseudomonas syringae pv. sesame. Three isolates inhibited the growth of X. campestris pv. campestris during in vitro screening. The crude extracts of two isolates (ASC3-2 and ASC5-7P) had a minimum inhibitory concentration (MIC) of 128 mg L-1against X. campestris pv. campestris. For isolate ACZ2-27, its crude extract showed stronger inhibitory effect with a lower MIC value of 64 mg L-1 against X. campestris pv. campestris. These three active isolates were identified as members of the genus Streptomyces based on their 16S rRNA gene sequences. Phylogenetic analysis based on the maximum likelihood algorithm showed that isolate ACZ2-27, ASC3-2 and ASC5-7P were closely related to Streptomyces misionensis NBRC 13063T (99.71%), Streptomyces cacaoi subsp. cacaoi NBRC 12748T (100%) and Streptomyces puniceus NBRC 12811T (100%), respectively. In addition, representative isolates from non-Streptomyces groups were identified by 16S rRNA gene sequence analysis. High similarities were found with members of the genera Actinomadura, Micromonospora and Nonomuraea. Our study provides evidence of actinomycetes associated with the black dwarf honey bee including members of rare genera. Antimicrobial potential of these insect associated Streptomyces was also demonstrated especially the antibacterial activity against phytopathogenic bacteria.

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).

Antimicrobial activity of Streptomyces spp. isolated from Apis dorsata combs against some phytopathogenic bacteria

The aim of this study was to investigate the antimicrobial potential of actinomycetes isolated from combs of the giant honey bee, Apis dorsata. In total, 25 isolates were obtained from three different media and were screened for antimicrobial activity against four plant pathogenic bacteria (Ralstonia solanacearum, Xanthomonas campestris pv. campestris, Xanthomonas oryzae pv. oryzae and Pectobacterium carotovorum). Following screening using a cross-streaking method, three isolates showed the potential to inhibit the growth of plant pathogenic bacteria. Based on a 96-well microtiter assay, the crude extract of DSC3-6 had minimum inhibitory concentration (MIC) values against X. oryzae pv. oryzae, X. campestris pv. campestris, R. solanacearum and P. carotovorum of 16, 32, 32 and 64 mg L^-1, respectively. The crude extract of DGA3-20 had MIC values against X. oryzae pv. oryzae, X. campestris pv. campestris, R. solanacearum and P. carotovorum of 32, 32, 32 and 64 mg L^-1, respectively. The crude extract of DGA8-3 at 32 mgL^-1 inhibited the growth of X. oryzae pv. oryzae, X. campestris pv. campestris, R. solanacearum and P. carotovorum. Based on their 16S rRNA gene sequences, all isolates were identified as members of the genus Streptomyces. The analysis of 16S rRNA gene sequence similarity and of the phylogenetic tree based on the maximum likelihood algorithm showed that isolates DSC3-6, DGA3-20 and DGA8-3 were closely related to Streptomyces ramulosus (99.42%), Streptomyces axinellae (99.70%) and Streptomyces drozdowiczii (99.71%), respectively. This was the first report on antibacterial activity against phytopathogenic bacteria from actinomycetes isolated from the giant honey bee.

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).

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).

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.

Natural Products from Actinobacteria Associated with Fungus-Growing Termites

The chemical analysis of insect-associated Actinobacteria has attracted the interest of natural product chemists in the past years as bacterial-produced metabolites are sought to be crucial for sustaining and protecting the insect host. The objective of our study was to evaluate the phylogeny and bioprospecting of Actinobacteria associated with fungus-growing termites. We characterized 97 Actinobacteria from the gut, exoskeleton, and fungus garden (comb) of the fungus-growing termite Macrotermes natalensis and used two different bioassays to assess their general antimicrobial activity. We selected two strains for chemical analysis and investigated the culture broth of the axenic strains and fungus-actinobacterium co-cultures. From these studies, we identified the previously-reported PKS-derived barceloneic acid A and the PKS-derived rubterolones. Analysis of culture broth yielded a new dichlorinated diketopiperazine derivative and two new tetracyclic lanthipeptides, named rubrominins A and B. The discussed natural products highlight that insect-associated Actinobacteria are highly prolific natural product producers yielding important chemical scaffolds urgently needed for future drug development programs.

Proposal to emend Rules 50a and 50b of the International Code of Nomenclature of Prokaryotes

Rules 50a and 50b of the International Code of Nomenclature of Prokaryotes respectively regulate the elevation of a subspecies to the rank of a species and the lowering of a species to the rank of subspecies. The Code does not indicate that the resulting new names must be considered new combinations, as the cases described in Rules 50a and 50b are not covered by Rule 34a. Based on the rules of the Code, new combination events are applicable only at the identical rank, and therefore new combination events and new species/subspecies events are mutually exclusive. In spite of this there have been at least 44 cases in which the new names were described as comb. nov. during elevation in rank from subspecies to species and at least 30 such cases during lowering in rank from species to subspecies. To prevent confusion in the future we propose adding notes to Rules 50a and 50b to clarify the issue.

Actinomadura hankyongense sp. nov. Isolated From Soil of Ginseng Cultivating Field

A Gram-positive, rod-shaped, non-spore-forming, and aerobic bacterium (Gsoil 556^T) was isolated from soil of a ginseng field and subjected to its taxonomic position. Based on 16S rRNA gene sequence similarity, strain Gsoil 556^T was shown to belong to the genus Actinomadura of the family Thermomonosporaceae and was closely related to A. montaniterrae CYP1-1B^T (99.3%), A. nitritigenes DSM 44137^T (98.7%), and A. rudentiformis HMC1^T (98.5%), while it showed less than 98.4% sequence similarity to the other species of this genus. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that it is most closely related to A. rudentiformis HMC1^T and A. nitritigenes DSM 44137^T. The DNA G+C content was 73.1 mol%. The peptidoglycan was meso-diaminopimelic acid and the whole-cell sugar contained fucose, galactose, glucose, mannose, and ribose. The predominant menaquinone (KK) was MK-9(H₈) [55%] and MK-9(H₆) [45%]. The major cellular fatty acids were C_14:0, C_16:0, C_18:1 ω9c and summed feature 3 (C_16:1 ω6c/C_16:1 ω7c). All these data supported the affiliation of strain Gsoil 556^T to the genus Actinomadura. The DNA-DNA hybridization between strain Gsoil 556^T and its phylogenetically closest relatives were less than 40%. Furthermore, the results of physiological and biochemical tests enabled strain Gsoil 556^T to be differentiated genotypically and phenotypically from currently known Actinomadura species. Therefore, strain Gsoil 556^T represents a novel species of the genus Actinomadura, for which the name Actinomadura hankyongense sp. nov. is proposed. The type strain Gsoil 556^T (=KACC 19438^T=LMG 30327^T).

Deciphering the late steps of rifamycin biosynthesis

Rifamycin-derived drugs, including rifampin, rifabutin, rifapentine, and rifaximin, have long been used as first-line therapies for the treatment of tuberculosis and other deadly infections. However, the late steps leading to the biosynthesis of the industrially important rifamycin SV and B remain largely unknown. Here, we characterize a network of reactions underlying the biosynthesis of rifamycin SV, S, L, O, and B. The two-subunit transketolase Rif15 and the cytochrome P450 enzyme Rif16 are found to mediate, respectively, a unique C–O bond formation in rifamycin L and an atypical P450 ester-to-ether transformation from rifamycin L to B. Both reactions showcase interesting chemistries for these two widespread and well-studied enzyme families.

The enzymes Rif15 and Rif16 are involved in the late steps of the biosynthesis of rifamycins, a group of antibiotics. Here, the authors characterized these two proteins and found that they catalyse unusual biochemical reactions.

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).

Actinomycetes with antimicrobial activity isolated from paper wasp (Hymenoptera: Vespidae: Polistinae) nests

Actinomycetes-a group of antimicrobial producing bacteria-have been successfully cultured and characterized from the nest material of diverse arthropods. Some are symbionts that produce antimicrobial chemicals found to protect nest brood and resources from pathogenic microbes. Others have no known fitness relationship with their associated insects, but have been found to produce antimicrobials in vitro. Consequently, insect nest material is being investigated as a new source of novel antimicrobial producing actinomycetes, which could be harnessed for therapeutic potential. To extend studies of actinomycete-insect associations beyond soil-substrate dwelling insects and wood boring excavators, we conducted a preliminary assessment of the actinomycetes within the nests of the paper wasp, Polistes dominulus (Christ). We found that actinomycetes were readily cultured from nest material across multiple invasive P. dominulus populations-including members of the genera Streptomyces, Micromonospora, and Actinoplanes. Thirty of these isolates were assayed for antimicrobial activity against the challenge bacteria Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, Serratia marcescens, and Bacillus subtilis. Sixty percent of isolates inhibited the growth of at least one challenge strain. This study provides the first assessment of bacteria associated with nests of P. dominulus, and the first record of antimicrobial producing actinomycetes isolated from social wasps. We provide a new system to explore nest associated actinomycetes from a ubiquitous and cosmopolitan group of insects.

Actinomadura xylanilytica sp. nov., an actinomycete isolated from soil

The taxonomic position of a soil isolate, strain BK147T, was established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological characteristics consistent with its classification in the genus Actinomadura . It formed a distinct phyletic line in the phylogenetic tree based on 16S rRNA gene sequences of members of the genus Actinomadura and was most closely, albeit loosely, related to Actinomadura bangladeshensis DSM 45347T, Actinomadura meyerae DSM 44715T and Actinomadura napierensis NRRL B-24319T but was readily distinguished from these strains using a range of phenotypic properties. Based on the combined genotypic and phenotypic data it is proposed that isolate BK147T ( = KACC 20919T = NCIMB 14771T = NRRL B-24852T) be classified as the type strain of a novel species of the genus Actinomadura , for which the name Actinomadura xylanilytica sp. nov. is proposed.

Actinomadura sediminis sp. nov., a marine actinomycete isolated from mangrove sediment

In this study, the taxonomic position of an actinobacterium, strain YIM M 10931T, which was isolated from a mangrove sediment sample collected in Dugong Creek, Little Andaman, India, was determined by a polyphasic approach. This Gram-positive, aerobic strain produced branched substrate mycelium and aerial hyphae, which differentiated into short, hooked or spiral spore chains. The organism contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The whole cell sugars consisted of mannose, ribose, glucose, galactose and madurose. The cellular fatty acid profile mainly consisted of iso-C16 : 0, 10-methyl C18 : 0 and C16 : 0. The quinone system was predominantly composed of MK-9(H8) (45.5 %) and MK-9(H6) (39 %). The phospholipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol and two unknown phospholipids. The organism showed a combination of morphological and chemotaxonomic properties typical of members of the genus Actinomadura . Moreover, phylogenetic analysis based on a 16S rRNA gene sequence generated from the strain identified its closest relatives as Actinomadura cremea DSM 43676T (98.4 % sequence similarity), Actinomadura rifamycini DSM 43936T (97.4 %) and Actinomadura apis IM17-1T (96.9 %). It was obvious from the resulting phylogenetic trees that strain YIM M 10931T belongs to a distinct subclade within the evolutionary radiation of the genus Actinomadura . DNA–DNA hybridizations of strain YIM M 10931T with A. cremea DSM 43676T and A. rifamycini DSM 43936T were performed and further confirmed that the isolate represents a separate genomic species. Based on the phenotypic and genotypic characteristics presented, it is proposed that strain YIM M 10931T represents a novel species within the genus Actinomadura , for which the name Actinomadura sediminis sp. nov. is proposed; the type strain is YIM M 10931T ( = CCTCC AA 2010009T = DSM 45500T).

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).

T-RFLP analysis of bacterial communities in the midguts of Apis mellifera and Apis cerana honey bees in Thailand

This study investigated bacterial community structures in the midguts of Apis mellifera and Apis cerana in Thailand to understand how bacterial communities develop in Apis species. The bacterial species present in replicate colonies from different locations and life stages were analysed. PCR amplification of bacterial 16S rRNA gene fragments and terminal restriction fragment length polymorphism analyses revealed a total of 16 distinct terminal restriction fragments (T-RFs), 12 of which were shared between A. mellifera and A. cerana populations. The T-RFs were affiliated to Beta- and Gammaproteobacteria, Firmicutes and Actinomycetes. The Gammaproteobacteria were found to be common in all stages of honey bee, but in addition, the Firmicutes group was found to be present in the worker bees. Bacterial community structure showed no difference amongst the replicate colonies, but was affected to some degree by geographical location, life stage and species of honey bees.

Actinomadura meridiana sp. nov., isolated from mountain soil

A novel actinomycete, designated strain DLS-45(T), was isolated from soil from the surface of a rock collected from the peak of Darangshi Oreum (Small Mountain) in Jeju, Republic of Korea. Substrate mycelium was well developed, but aerial mycelium was scant on most of the media tested. Spherical to subspherical spores on the aerial mycelium were in chains that were arranged in hooks and their surfaces were warty. The combination of morphological and chemical features supported the classification of the new isolate in the genus Actinomadura. The neighbour-joining tree based on 16S rRNA gene sequences showed that the strain belonged to the family Thermomonosporaceae and formed a coherent cluster with Actinomadura pelletieri IMSNU 22169(T) (98.0% sequence similarity). The other closest relatives were Actinomadura bangladeshensis 3-46-b(3)(T) (98.2%) and Actinomadura chokoriensis 3-25-a(11)(T) (97.9%). Levels of DNA-DNA relatedness between strain DLS-45(T) and the type strains of the phylogenetic relatives were less than 17%. A battery of phenotypic, genotypic and DNA-DNA relatedness data indicated that strain DLS-45(T) represented a novel species of the genus Actinomadura, for which the name Actinomadura meridiana sp. nov. is proposed. The type strain is strain DLS-45(T) (=KCTC 19558(T)=DSM 45252(T)).