Micromonospora fluminis sp. nov., isolated from mountain river sediment

During a bioprospection of bacteria with antimicrobial activity, the actinomycete strain A38^T was isolated from a sediment sample of the Carpintero river located in the Gran Piedra Mountains, Santiago de Cuba province (Cuba). This strain was identified as a member of the genus Micromonospora by means of a polyphasic taxonomy study. Strain A38^T was an aerobic Gram-positive filamentous bacterium that produced single spores in a well-developed vegetative mycelium. An aerial mycelium was absent. The cell wall contained meso-diaminopimelic acid and the whole-cell sugars were glucose, mannose, ribose and xylose. The major cellular fatty acids were isoC_15:0, 10 methyl C_17:0, anteiso-C_17:0 and iso-C_17:0. The predominant menaquinones were MK-10(H₄) and MK-10(H6). Phylogenetic analysis of 16S rRNA gene sequences revealed that this strain was closely related to Micromonospora tulbaghiae DSM 45142^T (99.5 %), Micromonospora citrea DSM 43903^T (99.4 %), Micromonospora marina DSM 45555^T (99.4 %), Micromonospora maritima DSM 45782^T (99.3 %), Micromonospora sediminicola DSM 45794^T (99.3 %), Micromonospora aurantiaca DSM 43813^T (99.2 %) and Micromonospora chaiyaphumensis DSM 45246^T (99.2 %). The results of OrthoANIu analysis showed the highest similarity to Micromonospora chalcea DSM 43026^T (96.4 %). However, the 16S rRNA and gyrB gene sequence-based phylogeny and phenotypic characteristics provided support to distinguish strain A38^T as a novel species. On the basis of the results presented here, we propose to classify strain A38^T (=LMG 30467^T=CECT 30034^T) as the type strain of the novel species Micromonospora fluminis sp. nov.

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential

There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.

Micromonospora yasonensis sp. nov., isolated from a Black Sea sediment

A Micromonospora strain, designated DS3186(T), isolated from sediment collected from the Black Sea off the Yason Peninsula, Ordu, Turkey, was examinated using a polyphasic approach. The strain was found to have chemotaxonomic, morphological and phylogenetic properties consistent with its clasification in the genus Micromonospora. A comparative 16S rRNA gene sequence analysis showed that the strain was closely related to the type strains of Micromonospora olivasterospora (99.0 %), Micromonospora equina (98.8 %), Micromonospora rhizosphaerae (98.8 %) and Micromonospora viridifaciens (98.8 %); low levels of DNA-DNA relatednes were found between the isolate and the M. olivasterospora and M. rhizosphaerae strains. Corresponding phylogenetic analysis based on partial gyrB gene sequences showed that strain DS3186(T) formed a subclade with the type strains of Micromonospora eburnea, M. equina, Micromonospora narathiwatensis and M. viridifaciens. Strain DS3186(T) was distinguished from its close phylogenetic neighbours using a combination of chemotaxonomic, morphological and physiological properties. Consequently, it is proposed that strain DS3186(T) represents a novel Micromonospora species for which the name Micromonospora yasonensis sp. nov. is proposed. The type strain is DS3186(T) (=DSM 45980(T) = KCTC 29433(T)).

Micromonospora zhanjiangensis sp. nov., isolated from mangrove forest soil

A novel actinomycete, designated strain 2902at01T was isolated from soil collected at a mangrove forest in Zhanjiang, Guangdong province, China. The strain was identified using a polyphasic classification method. The 16S rRNA gene sequence of strain 2902at01T showed the highest similarity to Micromonospora equina Y22T (98.3 %) and Micromonospora pattaloongensis TJ2-2T (98.1 %). Phylogenetic analysis based on the gyrB gene sequence also clearly showed that the strain was different from any previously discovered species of the genus Micromonospora. The characteristic whole-cell sugars were ribose and xylose. The cell-wall hydrolysates contained alanine, asparagine, glycine and meso-diaminopimelic acid. MK-10(H6) and MK-10(H8) were the major menaquinones of the novel strain. The predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. The characteristic polar lipids of strain 2902at01T were phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and diphosphatidylglycerol. The DNA G+C content was 70.2 mol%. DNA–DNA hybridization data combined with other physiological and biochemical features could distinguish strain 2902at01T from the reference strains M. equina Y22T and M. pattaloongensis TJ2-2 T. On the basis of these phenotypic and genotypic data, strain 2902at01T represents a novel species of the genus Micromonospora, for which the name Micromonospora zhanjiangensis sp. nov. is proposed. The type strain is 2902at01T ( = CCTCC AA2014018T = DSM 45902T).

Micromonospora nickelidurans sp. nov., isolated from soil from a nickel-mining site

An actinomycete, strain K55T, was isolated from a composite soil sample from a nickel mine, collected from Yueyang, Shaanxi Province, PR China. Strain K55T showed 16S rRNA gene sequence similarities of 98.73 %–98.51 % to species of the genus Micromonospora, including Micromonospora haikouensis 232617T, Micromonospora coxensis 2-30-b(28)T, Micromonospora wenchangensis 2602GPT1-05T, Micromonospora matsumotoense IMSNU 22003T, Micromonospora maoerensis NEAU-MES19T, and Micromonospora humi P0402T. This strain harboured meso-diaminopimelic acid, alanine and glycine as the major cell-wall amino acids, xylose and glucose as the characteristic whole-cell sugars, and iso-C15 : 0 (20.53 %),iso-C17 : 0 (12.74 %), iso-C16 : 0 (12.15 %), anteiso-C17 : 0 (7.97 %), C17 : 1ω8c (7.49 %) and C17 : 0 (6.63 %) as the dominant fatty acids. The major menaquinones were MK-10(H4) and MK-10(H6). The phospholipid profile comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol and unknown phosphoglycolipids. The DNA G+C content was 71.4 mol%. A comprehensive analysis of several physiological and biochemical traits and DNA–DNA relatedness indicated that strain K55T was different from closely related species. These phenotypic, genotypic and chemotaxonomic data suggest that strain K55T represents a novel species of the genus Micromonospora, for which the name Micromonospora nickelidurans sp. nov., is proposed. The type strain is K55T ( = JCM 30559T = ACCC19713T).

Micromonospora sonneratiae sp. nov., isolated from a root of Sonneratia apetala

A novel endophytic actinomycete, strain 274745(T), was isolated from a root of Sonneratia apetala collected in a mangrove forest in Sanya, Hainan province, China. The 16S rRNA gene sequence of strain 274745(T) showed the greatest similarity to Micromonospora pattaloongensis TJ2-2(T) (98.3 %). Phylogenetic analysis based on the gyrB gene also supported the close relationship of these two strains. The predominant menaquinone was MK-10(H8) and the major fatty acids were iso-C15 : 0, C17 : 0 and anteiso-C15 : 0. The characteristic whole-cell sugars were xylose and mannose. The cell wall contained meso-diaminopimelic acid and glycine. The polar lipid profile mainly comprised phosphatidylethanolamine, phosphatidylinositol and diphosphatidylglycerol. The DNA G+C content was 71.6 mol%. Furthermore, a combination of DNA-DNA relatedness and some physiological and biochemical properties indicated that the novel strain could be readily distinguished from the closest phylogenetic relatives. On the basis of these phenotypic and genotypic data, strain 274745(T) represents a novel species of the genus Micromonospora, for which the name Micromonospora sonneratiae sp. nov. is proposed. The type strain is 274745(T) ( = CCTCC AA 2012003(T) = DSM 45704(T)).