Amycolatopsis umgeniensis sp. nov., isolated from soil from the banks of the Umgeni River in South Africa

Amycolatopsis mongoliensis sp. nov., a novel actinobacterium with antifungal activity isolated from a coal mining site in Mongolia

A novel filamentous actinobacterium designated strain 4-36T showing broad-spectrum antifungal activity was isolated from a coal mining site in Mongolia, and its taxonomic position was determined using polyphasic approach. Optimum growth occurred at 30 °C, pH 7.5 and in the absence of NaCl. Aerial and substrate mycelia were abundantly formed on agar media. The colour of aerial mycelium was white and diffusible pigments were not formed. Phylogenetic analyses based on 16S rRNA gene sequence showed that strain 4-36T formed a distinct clade within the genus Amycolatopsis. The 16S rRNA gene sequence similarity showed that the strain was mostly related to Amycolatopsis lexingtonensis DSM 44544T and Amycolatopsis rifamycinica DSM 46095T with 99.3 % sequence similarity. However, the highest digital DNA-DNA hybridization value to closest species was 44.1 %, and the highest average nucleotide identity value was 90.2 %, both of which were well below the species delineation thresholds. Chemotaxonomic properties were typical of the genus Amycolatopsis, as the major fatty acids were C15 : 0, iso-C16 : 0 and C16 : 0, the cell-wall diamino acid was meso-diaminopimelic acid, the quinone was MK-9(H4), and the main polar lipids were diphosphatidylglycerol, phosphatidylmethanolamine and phosphatidylethanolamine. The in silico prediction of chemotaxonomic markers was also carried out by phylogenetic analysis. The genome mining for biosynthetic gene clusters of secondary metabolites in strain 4-36T revealed the presence of 34 gene clusters involved in the production of polyketide synthase, nonribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptide, lanthipeptide, terpenes, siderophore and many other unknown clusters. Strain 4-36T showed broad antifungal activity against several filamentous fungi. The phenotypic, biochemical and chemotaxonomic properties indicated that the strain could be clearly distinguished from other species of Amycolatopsis, and thus the name Amycolatopsis mongoliensis sp. nov. is proposed accordingly (type strain, 4-36T=KCTC 39526T=JCM 30565T).

Exogenous production of cold-active cellulase from polar Nocardiopsis sp. with increased cellulose hydrolysis efficiency

The present work was designed to isolate and characterise the actinobacteria in the Polar Front region of the Southern Ocean waters and species of Nocardiopsis and Streptomyces were identified. Among those, the psychrophilic actinobacterium, Nocardiopsis dassonvillei PSY13 was found to have good cellulolytic activity and it was further studied for the production and characterisation of cold-active cellulase enzyme. The latter was found to have a specific activity of 6.36 U/mg and a molar mass of 48 kDa with a 22.9-fold purification and 5% recovery at an optimum pH of 7.5 and a temperature of 10 °C. Given the importance of psychrophilic actinobacteria, N. dassonvillei PSY13 can be further exploited for its benefits, meaning that the Southern Ocean harbours biotechnologically important microorganisms that can be further explored for versatile biotechnological and industrial applications.

Amycolatopsis nivea sp. nov., isolated from a Yellow River sample

A novel actinobacterium, designated strain CFH S0261^T, was isolated from a sediment sample of the Yellow River. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of strain CFH S0261^T were Gram-reaction-positive, aerobic, non-motile. Growth occurs at 15-37 °C, pH 6.0-8.0 and with 0-9.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CFH S0261^T was a member of the genus Amycolatopsis. The 16S rRNA gene sequence similarity indicated that strain CFH S0261^T is most closely related to the type strains of Amycolatopsis niigatensis LC11^T (98.95 %), Amycolatopsis echigonensis LC2^T (98.81 %) and Amycolatopsis albidoflavus IMSNU 22139^T (98.73 %). The whole-genome of CFH S0261^T showed a G+C content of 69.5 mol%. The ANI values and in silico DDH values between CFH S0261^T and the other species of the genus Amycolatopsis were found to be low (ANIb <90.61 % and DDH <53.40 %). The cell wall diamino acid in the peptidoglycan of strain CFH S0261^T was meso-diaminopimelic acid and the whole-cell hydrolysate comprised arabinose, galactose, glucose, rhamnose and ribose. The predominant menaquinone was MK-9(H₄). The major cellular fatty acids were C_16 : 0, iso-C_15 : 0 and iso-C_16 : 0. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and four unidentified glycolipids. On the basis of phenotypic, genotypic and phylogenetic data, strain CFH S0261^T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis nivea sp. nov. is proposed. The type strain is CFH S0261^T (=KCTC 39515^T =CCTCC AA 2014028^T).

Bioinformatics delimitation of the psychrophilic and psychrotolerant actinobacteria isolated from the Polar Frontal waters of the Southern Ocean

Identification of microorganisms plays a key role in the determination of the composition of microbial diversity for bioprospecting of biotechnologically important biomolecules. Digitalization is the process that solve discrepancies in microbial identification and cataloguing their diversity in distinct ecological habitats. In view of this connection, the psychrophilic and psychrotolerant actinobacteria were isolated from the water samples of the Polar Frontal region of the Southern Ocean. 16S rRNA gene sequencing for identification of psychrophiles was carried out and sequences were deposited in NCBI GeneBank. 16S rRNA gene sequences were used to create QR codes, CGR, FCGR and GC plot. This generated digital data help to relate the diversity amongst the isolated actinobacterial strains. The digital data showed considerable divergence among the actinobacterial strains. This generated bioinformatics data is helpful in the delimitation of the psychrophilic and psychrotolerant actinobacteria. Thus, the present study is a robust and accurate method for the identification of Polar microorganisms in a fixed boundary. Hence, this work will help to assign a unique digital identity to microorganisms in near future [9-19].

A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus

The complete genome of methanol-utilizing Amycolatopsis methanolica strain 239^T was generated, revealing a single 7,237,391 nucleotide circular chromosome with 7074 annotated protein-coding sequences (CDSs). Comparative analyses against the complete genome sequences of Amycolatopsis japonica strain MG417-CF17^T, Amycolatopsis mediterranei strain U32 and Amycolatopsis orientalis strain HCCB10007 revealed a broad spectrum of genomic structures, including various genome sizes, core/quasi-core/non-core configurations and different kinds of episomes. Although polyketide synthase gene clusters were absent from the A. methanolica genome, 12 gene clusters related to the biosynthesis of other specialized (secondary) metabolites were identified. Complete pathways attributable to the facultative methylotrophic physiology of A. methanolica strain 239^T, including both the mdo/mscR encoded methanol oxidation and the hps/hpi encoded formaldehyde assimilation via the ribulose monophosphate cycle, were identified together with evidence that the latter might be the result of horizontal gene transfer. Phylogenetic analyses based on 16S rDNA or orthologues of AMETH_3452, a novel actinobacterial class-specific conserved gene against 62 or 18 Amycolatopsis type strains, respectively, revealed three major phyletic lineages, namely the mesophilic or moderately thermophilic A. orientalis subclade (AOS), the mesophilic Amycolatopsis taiwanensis subclade (ATS) and the thermophilic A. methanolica subclade (AMS). The distinct growth temperatures of members of the subclades correlated with corresponding genetic variations in their encoded compatible solutes. This study shows the value of integrating conventional taxonomic with whole genome sequence data.

Classification of thermophilic actinobacteria isolated from arid desert soils, including the description of Amycolatopsis deserti sp. nov

The taxonomic position of 26 filamentous actinobacteria isolated from a hyper-arid Atacama Desert soil and 2 from an arid Australian composite soil was established using a polyphasic approach. All of the isolates gave the diagnostic amplification product using 16S rRNA oligonucleotide primers specific for the genus Amycolatopsis. Representative isolates had chemotaxonomic and morphological properties typical of members of the genus Amycolatopsis. 16S rRNA gene analyses showed that all of the isolates belong to the Amycolatopsis methanolica 16S rRNA gene clade. The Atacama Desert isolates were assigned to one or other of two recognised species, namely Amycolatopsis ruanii and Amycolatopsis thermalba, based on 16S rRNA gene sequence, DNA:DNA relatedness and phenotypic data; emended descriptions are given for these species. In contrast, the two strains from the arid Australian composite soil, isolates GY024(T) and GY142, formed a distinct branch at the periphery of the A. methanolica 16S rRNA phyletic line, a taxon that was supported by all of the tree-making algorithms and by a 100 % bootstrap value. These strains shared a high degree of DNA:DNA relatedness and have many phenotypic properties in common, some of which distinguished them from all of the constituent species classified in the A. methanolica 16S rRNA clade. Isolates GY024(T) and GY142 merit recognition as a new species within the A. methanolica group of thermophilic strains. The name proposed for the new species is Amycolatopsis deserti sp. nov.; the type strain is GY024(T) (=NCIMB 14972(T) = NRRL B-65266(T)).

Amycolatopsis rhabdoformis sp. nov., an actinomycete isolated from a tropical forest soil

Strain SB026T was isolated from Brazilian rainforest soil and its taxonomic position established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological features consistent with its classification in the genus Amycolatopsis and formed a branch in the Amycolatopsis 16S rRNA gene tree together with Amycolatopsis bullii NRRL B-24847T, Amycolatopsis plumensis NRRL B-24324T, Amycolatopsis tolypomycina DSM 44544T and Amycolatopsis vancoresmycina NRRL B-24208T. It was related most closely to A. bullii NRRL B-24847T (99.0 % 16S rRNA gene sequence similarity), but was distinguished from this strain by a low level of DNA–DNA relatedness (~46 %) and discriminatory phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the isolate should be classified in the genus Amycolatopsis as representing a novel species, Amycolatopsis rhabdoformis sp. nov. The type strain is SB026T ( = CBMAI 1694T = CMAA 1285T = NCIMB 14900T).

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors’ names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.