“…Isolates LB4 and LB41 were found to have identical concatenated gene sequences and showed an MLSA genetic distance with M . chalcea DSM 43026 T of 0.002% (Table S1), a value well below the species level threshold of ≤0.007 proposed by Rong and Huang 47,48 and equivalent to the 70% DNA:DNA cut-off point recommended for the delineation of prokaryotic species 49 . In contrast, the two isolates shared genetic distances above the recommended threshold with all of the other closely related phylogenetic neighbours.Figure 2Neighbour-joining phylogenetic tree based on multilocus sequence alignment of 16S rRNA, gyr B, rpo B, atp D, and rec A gene sequences showing relationships between the isolates and between them and Micromonospora type strains.…”
Section: Resultsmentioning
confidence: 75%
“…In contrast, it is clear that isolate LB19 belongs to the species M . ureilytica as the two strains share a distance score of 0.005, well below the cut-off point for assigning strains to the same species 47,48 . On the same basis, it is evident from Table S1 that isolate LB39 T shows distance scores with its nearest relatives above the 0.007 threshold and thereby merits consideration as a new Micromonospora species.…”
The taxonomic status, biotechnological and ecological potential of several Micromonospora strains isolated from an extreme hyper arid Atacama Desert soil were determined. Initially, a polyphasic study was undertaken to clarify the taxonomic status of five micromonosporae, strains LB4, LB19, LB32T, LB39T and LB41, isolated from an extreme hyper-arid soil collected from one of the driest regions of the Atacama Desert. All of the isolates were found to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Micromonospora. Isolates LB32T and LB39T were distinguished from their nearest phylogenetic neighbours and proposed as new species, namely as Micromonospora arida sp. nov. and Micromonospora inaquosa sp. nov., respectively. Eluted methanol extracts of all of the isolates showed activity against a panel of bacterial and fungal indicator strains, notably against multi-drug resistant Klebsiella pneumoniae ATCC 700603 while isolates LB4 and LB41 showed pronounced anti-tumour activity against HepG2 cells. Draft genomes generated for the isolates revealed a rich source of novel biosynthetic gene clusters, some of which were unique to individual strains thereby opening up the prospect of selecting especially gifted micromonosporae for natural product discovery. Key stress-related genes detected in the genomes of all of the isolates provided an insight into how micromonosporae adapt to the harsh environmental conditions that prevail in extreme hyper-arid Atacama Desert soils.
“…Isolates LB4 and LB41 were found to have identical concatenated gene sequences and showed an MLSA genetic distance with M . chalcea DSM 43026 T of 0.002% (Table S1), a value well below the species level threshold of ≤0.007 proposed by Rong and Huang 47,48 and equivalent to the 70% DNA:DNA cut-off point recommended for the delineation of prokaryotic species 49 . In contrast, the two isolates shared genetic distances above the recommended threshold with all of the other closely related phylogenetic neighbours.Figure 2Neighbour-joining phylogenetic tree based on multilocus sequence alignment of 16S rRNA, gyr B, rpo B, atp D, and rec A gene sequences showing relationships between the isolates and between them and Micromonospora type strains.…”
Section: Resultsmentioning
confidence: 75%
“…In contrast, it is clear that isolate LB19 belongs to the species M . ureilytica as the two strains share a distance score of 0.005, well below the cut-off point for assigning strains to the same species 47,48 . On the same basis, it is evident from Table S1 that isolate LB39 T shows distance scores with its nearest relatives above the 0.007 threshold and thereby merits consideration as a new Micromonospora species.…”
The taxonomic status, biotechnological and ecological potential of several Micromonospora strains isolated from an extreme hyper arid Atacama Desert soil were determined. Initially, a polyphasic study was undertaken to clarify the taxonomic status of five micromonosporae, strains LB4, LB19, LB32T, LB39T and LB41, isolated from an extreme hyper-arid soil collected from one of the driest regions of the Atacama Desert. All of the isolates were found to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Micromonospora. Isolates LB32T and LB39T were distinguished from their nearest phylogenetic neighbours and proposed as new species, namely as Micromonospora arida sp. nov. and Micromonospora inaquosa sp. nov., respectively. Eluted methanol extracts of all of the isolates showed activity against a panel of bacterial and fungal indicator strains, notably against multi-drug resistant Klebsiella pneumoniae ATCC 700603 while isolates LB4 and LB41 showed pronounced anti-tumour activity against HepG2 cells. Draft genomes generated for the isolates revealed a rich source of novel biosynthetic gene clusters, some of which were unique to individual strains thereby opening up the prospect of selecting especially gifted micromonosporae for natural product discovery. Key stress-related genes detected in the genomes of all of the isolates provided an insight into how micromonosporae adapt to the harsh environmental conditions that prevail in extreme hyper-arid Atacama Desert soils.
“…MLSA have been found to clarify relationships between closely related streptomycetes because of the strong phylogenetic signal provided by partial sequences of single-copy house-keeping genes (Rong and Huang 2012, 2014; Labeda 2011, 2016, Labeda et al 2014, 2016, 2017); In the present MLSA analysis, the relationships found between isolate H9 T and the type strains of closely related Streptomyces species are shown in Fig. 3 and Table 3.…”
Section: Resultsmentioning
confidence: 65%
“…Despite being the largest genus in the domain Bacteria the taxon remains underspeciated (Okoro et al 2009; Antony-Babu et al 2010; Busarakam 2014). New species are assigned to the genus using a combination of genotype and phenotype properties, and some recent studies have featured MLSA (Rong and Huang 2012, 2014; Labeda et al 2014, 2017; Labeda 2016). …”
A polyphasic study was undertaken to determine the taxonomic status of a Streptomyces strain which had been isolated from a high altitude Atacama Desert soil and shown to have bioactive properties. The strain, isolate H9T, was found to have chemotaxonomic, cultural and morphological properties that place it in the genus Streptomyces. 16S rRNA gene sequence analyses showed that the isolate forms a distinct branch at the periphery of a well-delineated subclade in the Streptomyces 16S rRNA gene tree together with the type strains of Streptomyces crystallinus, Streptomyces melanogenes and Streptomyces noboritoensis. Multi-locus sequence analysis (MLSA) based on five house-keeping gene alleles showed that isolate H9T is closely related to the latter two type strains and to Streptomyces polyantibioticus NRRL B-24448T. The isolate was distinguished readily from the type strains of S. melanogenes, S. noboritoensis and S. polyantibioticus using a combination of phenotypic properties. Consequently, the isolate is considered to represent a new species of Streptomyces for which the name Streptomyces aridus sp. nov. is proposed; the type strain is H9T (=NCIMB 14965T=NRRL B65268T). In addition, the MLSA and phenotypic data show that the S. melanogenes and S. noboritoensis type strains belong to a single species, it is proposed that S. melanogenes be recognised as a heterotypic synonym of S. noboritoensis for which an emended description is given.Electronic supplementary materialThe online version of this article (doi:10.1007/s10482-017-0838-2) contains supplementary material, which is available to authorized users.
“…Universal primers 27f and 1525r were used for the 16S rRNA gene amplification (Lane 1991). For Multi-Locus Sequence Analysis (MLSA) genes, the set of primers previously reported were used (Rong and Huang 2014). One set of extra primers for the gene secY (Adekambi et al 2011) was modified and included for the MLSA studies.…”
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.
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