Catellatospora tagetis sp. nov., isolated from the root of a marigold (Tagetes erecta L.).

A Gram-stain positive, non-motile, mesophilic actinomycete, designated strain NEAU-YJC4(T) was isolated from the root of a marigold (Tagetes erecta L.) collected in Heilongjiang Province, northeast China, and characterized using a polyphasic approach. Morphological and chemotaxonomic properties of strain NEAU-YJC4(T) were consistent with the description of the genus Catellatospora. 16S rRNA gene sequence similarity studies showed that strain NEAU-YJC4(T) belongs to the genus Catellatospora, being most closely related to Catellatospora bangladeshensis JCM 12949(T) (98.7 %). Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain NEAU-YJC4(T) formed a monophyletic clade with the closest relative. A combination of DNA-DNA hybridization results and some phenotypic characteristics indicated that strain NEAU-YJC4(T) can be distinguished from C. bangladeshensis JCM 12949(T). Therefore, it is proposed that strain NEAU-YJC4(T) represents a novel species of the genus Catellatospora, for which the name Catellatospora tagetis sp. nov. is proposed. The type strain is NEAU-YJC4(T) (=CGMCC 4.7176(T) = JCM 30053(T)).

Dactylosporangium cerinum sp. nov., a novel actinobacterium isolated from the rhizosphere of Pinus koraiensis Sieb. et Zucc.

A novel actinobacterium, designated strain NEAU-TPG4(T) was isolated from rhizosphere soil of Pinus koraiensis Sieb. et Zucc. collected from Luobei, Heilongjiang Province, north China, and characterized using a polyphasic approach. Morphological and chemotaxonomic properties of strain NEAU-TPG4(T) were consistent with the description of the genus Dactylosporangium. The strain formed finger-shaped sporangia on short sporangiophores that emerged directly from substrate hyphae. The cell-wall peptidoglycan consisted of meso- and 3-hydroxy-diaminopimelic acids; arabinose, xylose and glucose were found as whole-cell sugars. The phospholipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinones were identified as MK-9(H8) and MK-9(H6). The predominant cellular fatty acids were identified as iso-C16:0, anteiso-C15:0, anteiso-C17:0 and C18:0. Phylogenetic analysis using 16S rRNA gene sequences also indicated that the strain should be classified in the genus Dactylosporangium and showed that the closest relatives were Dactylosporangium maewongense Japan Collection of Microorganism (JCM) 15933(T) (99.6 %), Dactylosporangium siamense NBRC 106093(T) (99.6 %), Dactylosporangium aurantiacum JCM 3083(T) (99.5 %) and Dactylosporangium luteum JCM 17685(T) (99.5 %). However, the low level of DNA-DNA relatedness and several cultural and physiological characteristics allowed the strain to be distinguished from its closest relatives. Thus, it is proposed that strain NEAU-TPG4(T) represents a novel Dactylosporangium species. Dactylosporangium cerinum sp. nov. The type strain of D. cerinum is NEAU-TPG4(T) (=CGMCC 4.7152(T) = DSM 46712(T)).

CRISPR-Cas systems in the marine actinomycete Salinispora: linkages with phage defense, microdiversity and biogeography.

BACKGROUND: Prokaryotic CRISPR-Cas systems confer resistance to viral infection and thus mediate bacteria-phage interactions. However, the distribution and functional diversity of CRISPRs among environmental bacteria remains largely unknown. Here, comparative genomics of 75 Salinispora strains provided insight into the diversity and distribution of CRISPR-Cas systems in a cosmopolitan marine actinomycete genus. RESULTS: CRISPRs were found in all Salinispora strains, with the majority containing multiple loci and different Cas array subtypes. Of the six subtypes identified, three have not been previously described. A lower prophage frequency in S. arenicola was associated with a higher fraction of spacers matching Salinispora prophages compared to S. tropica, suggesting differing defensive capacities between Salinispora species. The occurrence of related prophages in strains from distant locations, as well as spacers matching those prophages inserted throughout spacer arrays, indicate recurring encounters with widely distributed phages over time. Linkages of CRISPR features with Salinispora microdiversity pointed to subclade-specific contacts with mobile genetic elements (MGEs). This included lineage-specific spacer deletions or insertions, which may reflect weak selective pressures to maintain immunity or distinct temporal interactions with MGEs, respectively. Biogeographic patterns in spacer and prophage distributions support the concept that Salinispora spp. encounter localized MGEs. Moreover, the presence of spacers matching housekeeping genes suggests that CRISPRs may have functions outside of viral defense. CONCLUSIONS: This study provides a comprehensive examination of CRISPR-Cas systems in a broadly distributed group of environmental bacteria. The ubiquity and diversity of CRISPRs in Salinispora suggests that CRISPR-mediated interactions with MGEs represent a major force in the ecology and evolution of this cosmopolitan marine actinomycete genus.

Catellatospora aurea sp. nov., a novel actinomycete isolated from soil.

A novel actinomycete, designated strain NEAU-SH16(T) was isolated from a soil sample collected from the riverbank of Wusong river in Shanghai and characterized using a polyphasic approach. Morphological and chemotaxonomic properties of strain NEAU-SH16(T) were consistent with the description of the genus Catellatospora. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain NEAU-SH16(T) formed a distinct branch with the closest relatives Catellatospora coxensis DSM 44901(T) (99.2 %) and Catellatospora citrea DSM 44097(T) (99.0 %), an association that was supported by a bootstrap value of 78 % in the neighbour-joining tree and also recovered with the maximum-likelihood algorithm. However, the low level of DNA-DNA relatedness and some different physiological characteristics allowed the strain to be distinguished from its closest relatives. Thus, it is proposed that strain NEAU-SH16(T) represents a novel Catellatospora species. Catellatospora aurea sp. nov. The type strain of Catellatospora aurea is NEAU-SH16(T) (=CGMCC 4.7147(T) = DSM 46719(T)).

Actinoplanes hulinensis sp. nov., a novel actinomycete isolated from soybean root (Glycine max (L.) Merr).

A novel actinomycete, designated strain NEAU-M9(T), was isolated from soybean root (Glycine max (L.) Merr) and characterized using a polyphasic approach. 16S rRNA gene sequence similarity studies showed that strain NEAU-M9(T) belonged to the genus Actinoplanes, being most closely related to Actinoplanes campanulatus DSM 43148(T) (98.85 %), Actinoplanes capillaceus DSM 44859(T) (98.70 %), Actinoplanes lobatus DSM 43150(T) (98.30 %), Actinoplanes auranticolor DSM 43031(T) (98.23 %) and Actinoplanes sichuanensis 03-723(T) (98.06 %); similarity to other type strains of the genus Actinoplanes ranged from 95.87 to 97.56 %. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that the isolate formed a distinct phyletic line with A. campanulatus DSM 43148(T) and A. capillaceus DSM 44859(T). This branching pattern was also supported by the tree constructed with the maximum-likelihood method. However, the low level of DNA-DNA relatedness allowed the isolate to be differentiated from the above-mentioned two Actinoplanes species. Moreover, strain NEAU-M9(T) could also be distinguished from the most closely related species by morphological, physiological and characteristics. Therefore, it is proposed that strain NEAU-M9(T) represents a novel Actinoplanes species, Actinoplanes hulinensis sp. nov. The type strain of Actinoplanes hulinensis is NEAU-M9(T) (= CGMCC 4.7036(T) = DSM 45728(T)).

Salinispora pacifica sp. nov., an actinomycete from marine sediments.

A polyphasic analysis was carried out to clarify the taxonomic status of four marine actinomycete strains that share a phylogenetic relationship and phenotypic characteristics with the genus Salinispora. These strains formed a distinct lineage within the Salinispora 16S rRNA and gyrB trees and were found to possess a range of phenotypic properties and DNA:DNA hybridization values that distinguished them from the type strains of the two validly named species in this genus, Salinispora tropica (CNB-440(T), ATCC BAA-916(T)) and Salinispora arenicola (CNH-643(T), ATCC BAA-917(T)). The combined genotypic and phenotypic data support this conclusion. It is proposed that the strains be designated as Salinispora pacifica sp. nov., the type strain of which is CNR-114(T) (DSMZ YYYYT = KACC 17160(T)).

Genetic complementation of the obligate marine actinobacterium Salinispora tropica with the large mechanosensitive channel gene mscL rescues cells from osmotic downshock.

Marine actinomycetes in the genus Salinispora fail to grow when seawater is replaced with deionized (DI) water in complex growth media. While bioinformatic analyses have led to the identification of a number of candidate marine adaptation genes, there is currently no experimental evidence to support the genetic basis for the osmotic requirements associated with this taxon. One hypothesis is that the lineage-specific loss of mscL is responsible for the failure of strains to grow in media prepared with DI water. The mscL gene encodes a conserved transmembrane protein that reduces turgor pressure under conditions of acute osmotic downshock. In the present study, the mscL gene from a Micromonospora strain capable of growth on media prepared with DI water was transformed into S. tropica strain CNB-440. The single-copy, chromosomal genetic complementation yielded a recombinant Salinispora mscL(+) strain that demonstrated an increased capacity to survive osmotic downshock. The enhanced survival of the S. tropica transformant provides experimental evidence that the loss of mscL is associated with the failure of Salinispora spp. to grow in low-osmotic-strength media.

Verrucosispora maris sp. nov., a novel deep-sea actinomycete isolated from a marine sediment which produces abyssomicins.

Verrucosispora isolate AB-18-032(T), the abyssomicin- and proximicin-producing actinomycete, has chemotaxonomic and morphological properties consistent with its classification in the genus Verrucosispora. The organism formed a distinct phyletic line in the Verrucosispora 16S rRNA gene tree sharing similarities of 99.7%, 98.7% and 98.9% with Verrucosispora gifhornensis DSM 44337(T), Verrucosispora lutea YIM 013(T) and Verrucosispora sediminis MS 426(T), respectively. It was readily distinguished from the two latter species using a range of phenotypic features and from V. gifhornensis DSM 44337(T), its nearest phylogenetic neighbor, by a DNA G+C content of 65.5 mol% obtained by thermal denaturation and fluorometry and DNA:DNA relatedness values of 64.0% and 65.0% using renaturation and fluorometric methods, respectively. It is apparent from the combined genotypic and phenotypic data that strain AB-18-032(T) should be classified in the genus Verrucosispora as a new species. The name Verrucosispora maris sp. nov. is proposed for this taxon with isolate AB-18-032(T) (= DSM 45365(T) = NRRL B-24793(T)) as the type strain.

Characterization of Actinoplanes missouriensis spore flagella.

Actinoplanes missouriensis spores swim with a tuft of flagella. Flagella of newborn spores are wrapped with a membranous sheath. When the sheath is unwrapped, spores start swimming. Flagellar length is kept short, at around 1.9 µm, which covers half the circumference of the spore.

Longispora fulva sp. nov., isolated from a forest soil, and emended description of the genus Longispora.

A novel actinomycete, strain KZ0017(T), was isolated from a forest soil collected in Ohnuma, Fukushima, Japan. Strain KZ0017(T) formed spore chains borne on top of short sporophores arising from vegetative hyphae. Spores were non-motile and cylindrical with smooth surfaces. Strain KZ0017(T) contained meso-diaminopimelic (A(2)pm) acid, 3-OH A(2)pm, d-glutamic acid, glycine and l-alanine in the cell-wall peptidoglycan, and xylose, mannose, galactose, rhamnose and ribose in cell-wall hydrolysates. The acyl type of the cell-wall polysaccharides was glycolyl. The predominant menaquinones were MK-10(H(4)) and MK-10(H(6)); MK-10(H(8)) was a minor component. The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol and several unknown lipids and glycolipids. The major fatty acids were iso-C(16 : 0), 10-methyl-C(17 : 0) and iso-C(17 : 1)ω9c. The DNA G+C content was 70.7 mol%. The 16S rRNA gene sequence of the isolate formed a monophyletic cluster with the single member of the genus Longispora in the family Micromonosporaceae. On the basis of morphological, chemotaxonomic and phylogenetic properties, strain KZ0017(T) represents a novel species of the genus Longispora, for which the name Longispora fulva sp. nov. is proposed; the type strain is KZ0017(T) ( = NBRC 105670(T) = DSM 45356(T)).

Planosporangium mesophilum sp. nov., isolated from rhizosphere soil of Bletilla striata.

A Gram-stain-positive, non-motile actinomycete, designated strain YIM 48875(T), was isolated from rhizosphere soil of Bletilla striata and its taxonomic position was established by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain YIM 48875(T) belonged to the genus Planosporangium, supported by a bootstrap value of 100 %. Cells of strain YIM 48875(T) showed two kinds of sporangia, which also supported its classification in the genus Planosporangium. Strain YIM 48875(T) grew optimally at 28 °C, at pH 6.0-8.0 and in the presence of 2 % (w/v) NaCl. The level of 16S rRNA gene sequence similarity between strain YIM 48875(T) and Planosporangium flavigriseum YIM 46034(T) was 98.6 %. Strain YIM 48875(T) exhibited a quinone system with menaquinones MK-9(H(4)), MK-9(H(6)) and MK-9(H(8)) as the predominant compounds, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol mannoside and the major fatty acids iso-C(15 : 0) and iso-C(16 : 0); these data were markedly different from those for P. flavigriseum YIM 46034(T). The level of DNA-DNA relatedness between strain YIM 48875(T) and P. flavigriseum YIM 46034(T) was 45.5 %. It is apparent from the genotypic and phenotypic data that strain YIM 48875(T) represents a novel species of the genus Planosporangium, for which the name Planosporangium mesophilum sp. nov. is proposed. The type strain is YIM 48875(T) ( = CCTCC AA 209049(T)  = KCTC 19779(T)).

Marine Sediment Recovered Salinispora sp. Inhibits the Growth of Emerging Bacterial Pathogens and other Multi-Drug-Resistant Bacteria.

Marine obligate actinobacteria produce a wide variety of secondary metabolites with biological activity, notably those with antibiotic activity urgently needed against multi-drug-resistant bacteria. Seventy-five marine actinobacteria were isolated from a marine sediment sample collected in Punta Arena de La Ventana, Baja California Sur, Mexico. The 16S rRNA gene identification, Multi Locus Sequence Analysis, and the marine salt requirement for growth assigned seventy-one isolates as members of the genus Salinispora, grouped apart but related to the main Salinispora arenicola species clade. The ability of salinisporae to inhibit bacterial growth of Staphylococcus epidermidis, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacer baumannii, Pseudomonas aeruginosa, and Enterobacter spp. was evaluated by cross-streaking plate and supernatant inhibition tests. Ten supernatants inhibited the growth of eight strains of S. epidermidis from patients suffering from ocular infections, two out of the eight showed growth inhibition on ten S. epidermidis strains from prosthetic joint infections. Also, it inhibited the growth of the remaining six multi-drug-resistant bacteria tested. These results showed that some Salinispora strains could produce antibacterial compounds to combat bacteria of clinical importance and prove that studying different geographical sites uncovers untapped microorganisms with metabolic potential.

Virgisporangium myanmarense sp. nov., a novel motile actinomycete isolated from an anthill soil in Myanmar.

An actinomycete strain, designated MM04-1133T, was isolated from an anthill soil sample collected in Bagan, Myanmar. To establish the taxonomic status of this strain, the isolate was subjected to a polyphasic approach. Strain MM04-1133T was Gram-staining positive, aerobic, motile and formed long and narrow sporangia directly above the surface of the substrate mycelium. Whole-cell hydrolysates of the strain contained 3-OH-diaminopimelic acid, arabinose, glucose, galactose, mannose, rhamnose and xylose. The predominant menaquinones were MK-10(H6) and MK-10(H8). The major cellular fatty acids were iso-C16:0 and anteiso-C17:0. The diagnostic phospholipid was phosphatidylethanolamine. The G+C content of the DNA was 69.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain MM04-1133T clustered within the genus Virgisporangium, with the sequence exhibiting highest similarity (98.5% identity) with Virgisporangium ochraceum NBRC 16418T. The strain grew in the presence of 0-1% (w/v) NaCl, at pH 5-8 and at 20-40 °C, with optimal growth at 30-37 °C. Based on phylogenetic analysis and chemotaxonomic and phenotypic data, we propose classifying this isolate as a novel species of the genus Virgisporangium, to be designated as Virgisporangium myanmarense sp. nov. The type strain is MM04-1133T (=NBRC 112733T=VTCC 910008T).

Competitive strategies differentiate closely related species of marine actinobacteria.

Although competition, niche partitioning, and spatial isolation have been used to describe the ecology and evolution of macro-organisms, it is less clear to what extent these principles account for the extraordinary levels of bacterial diversity observed in nature. Ecological interactions among bacteria are particularly challenging to address due to methodological limitations and uncertainties over how to recognize fundamental units of diversity and link them to the functional traits and evolutionary processes that led to their divergence. Here we show that two closely related marine actinomycete species can be differentiated based on competitive strategies. Using a direct challenge assay to investigate inhibitory interactions with members of the bacterial community, we observed a temporal difference in the onset of inhibition. The majority of inhibitory activity exhibited by Salinispora arenicola occurred early in its growth cycle and was linked to antibiotic production. In contrast, most inhibition by Salinispora tropica occurred later in the growth cycle and was more commonly linked to nutrient depletion or other sources. Comparative genomics support these differences, with S. arenicola containing nearly twice the number of secondary metabolite biosynthetic gene clusters as S. tropica, indicating a greater potential for secondary metabolite production. In contrast, S. tropica is enriched in gene clusters associated with the acquisition of growth-limiting nutrients such as iron. Coupled with differences in growth rates, the results reveal that S. arenicola uses interference competition at the expense of growth, whereas S. tropica preferentially employs a strategy of exploitation competition. The results support the ecological divergence of two co-occurring and closely related species of marine bacteria by providing evidence they have evolved fundamentally different strategies to compete in marine sediments.

Characterization of maltose and maltotriose transport in the acarbose-producing bacterium Actinoplanes sp.

Acarbose, a pseudomaltotetraose, is produced by strains of the genus Actinoplanes. The compound is an inhibitor of alpha-glucosidases and is used in the treatment of patients suffering from type II diabetes. The benefits of acarbose for the producer are not known; however, a role as carbophor has been proposed. Acarbose synthesis is induced in the presence of maltose and maltotriose. We have investigated the transport activities for these sugars in Actinoplanes sp. strain SN 223/29 grown on different carbon sources, including acarbose. Under the conditions used, Actinoplanes sp. utilized acarbose as sole source of carbon and energy, although growth ceased after 24 h, possibly due to the accumulation of a toxic degradation product in the cytosol. Maltose transport was observed in cells grown on each of the substrates tested except glucose. Maltose transport of acarbose-grown cells was inhibited by sucrose and trehalose and, to a lesser extent, by maltodextrins but not by acarbose. In contrast, in maltose/maltotriose-grown cells maltose uptake was inhibited by acarbose. Maltotriose uptake in these cells was less inhibited by maltose but was more sensitive to acarbose than in acarbose-grown cells. The Km and Vmax values of maltose uptake are in the range of those reported for binding protein-dependent sugar ATP-binding cassette (ABC) transport systems. A maltose-binding protein that does not bind acarbose was isolated from cells grown on either acarbose, glycerol or maltose. These results suggest that an acarbose-insensitive maltose/sucrose/trehalose transporter that also accepts maltodextrins operates in acarbose-grown cells while a maltodextrin transporter that accepts maltose/sucrose/trehalose and is moderately sensitive to acarbose is found in cells grown in maltose/maltotriose-containing media.

Dactylosporangium sucinum sp. nov., isolated from Thai peat swamp forest soil.

The actinomycete strain RY35-23(T) was isolated from peat swamp forest soil in Thailand. The taxonomic position of this strain was determined using polyphasic approach. Strain RY35-23(T) showed typical morphology and chemical properties similar to the members in the genus Dactylosporangium. On the basis of 16S ribosomal RNA gene analysis, this strain was closely related to Dactylosporangium fulvum JCM 5631(T) (98.94%), D. roseum JCM 3364(T) (98.87%) and D. darangshiense JCM 17441(T) (98.86%). The DNA-DNA relatedness between strain RY35-23(T) and its closely related species was lower than 70%, the cutoff level for assigning strains to the same species. On the basis of these results mentioned, the strain RY35-23(T) could be distinguished from its closely related type strains and represents a novel species of the genus Dactylosporangium, for which the name Dactylosporangium sucinum (type strain RY35-23(T)=JCM 19831(T)=TISTR 2212(T)=PCU 333(T)) is proposed.

Physiology of some actinomycete genera.

Actinomycetes are widespread in the environment and are mainly organotrophic. Studies of their ecology have been primarily focussed on their detection and isolation, with comparatively little attention to the control mechanisms that determine their occurrence and behaviour in their natural environments. This session provided some diverse examples of approaches to this problem. Several actinomycete genera produce motile spores. The significance of flagella proteins and factors influencing spore motility and germination are considered. The genus Frankia forms nitrogen-fixing associations with non-leguminous plants. Molecular techniques have been used to clarify the endophyte-host relationships. Micromonospora species are common in the environment. The growth and physiology of a gentamicin-producing strain are described. Thermophilic actinomycetes in the genus Thermoactinomyces are common in composts and other self-heating environments. Novel isolates from acid soil, which grow and produce enzymes active at high temperatures and in acidic conditions, are discussed.

Actinoplanes utahensis ZJB-08196 fed-batch fermentation at elevated osmolality for enhancing acarbose production.

Acarbose, a potent α-glucosidase inhibitor, is as an oral anti-diabetic drug for treatment of the type two, noninsulin-dependent diabetes. Actinoplanes utahensis ZJB-08196, an osmosis-resistant actinomycete, had a broad osmolality optimum between 309 mOsm kg(-1) and 719 mOsm kg(-1). Utilizing this unique feature, an fed-batch culture process under preferential osmolality was constructed through intermittently feeding broths with feed medium consisting of 14.0 g l(-1) maltose, 6.0 g l(-1) glucose and 9.0 g l(-1) soybean meal, at 48 h, 72 h, 96 h and 120 h. This intermittent fed-batch culture produced a peak acarbose titer of 4878 mg l(-1), increased by 15.9% over the batch culture.

Actinaurispora siamensis gen. nov., sp. nov., a new member of the family Micromonosporaceae.

Two actinomycete strains, CM2-8(T) and CM2-12, were isolated from temperate peat swamp forest soil in Chiang Mai Province, Thailand. Their taxonomic positions were determined using a polyphasic approach. Chemotaxonomic characteristics of these strains coincided with those of the family Micromonosporaceae, i.e. cell wall chemotype II, N-glycolyl type of muramic acid, and type II phospholipids. Phylogenetic analysis based on 16S rRNA gene sequence data also indicated that these strains fell within the family Micromonosporaceae and formed a distinct taxon in the Micromonosporaceae phylogenetic tree. On the basis of phylogenetic analysis, characteristic patterns of 16S rRNA gene signature nucleotides and chemotaxonomic data, it is proposed that the novel isolates belong to a new genus, Actinaurispora gen. nov. The type species of the genus is proposed as Actinaurispora siamensis sp. nov., with strain CM2-8(T) (=JCM 15677(T)=BCC 34762(T)) as the type strain.

Dactylosporangium maewongense sp. nov., isolated from soil.

Morphological and chemotaxonomic characterization of actinomycete strain MW2-25(T), isolated from tropical forest soil in Nakhon Sawan Province, Thailand, clearly demonstrated that this strain belongs to the genus Dactylosporangium. Phylogenetic analysis using 16S rRNA gene sequences also indicated that this strain should be classified in the genus Dactylosporangium and showed that the closest relative was Dactylosporangium aurantiacum IFO 12592(T) (99.3 % sequence similarity). DNA-DNA hybridization values and some physiological and biochemical properties indicated that this strain could be readily distinguished from its closest phylogenetic relatives. On the basis of these phenotypic and genotypic data, this strain represents a novel species, for which the name Dactylosporangium maewongense sp. nov. is proposed. The type strain is MW2-25(T) (=BCC 34832(T)=JCM 15933(T)).