Amycolatopsis bartoniae sp. nov. and Amycolatopsis bullii sp. nov., mesophilic actinomycetes isolated from arid Australian soils

New insights into the relationship between the average nucleotide identity and the digital DNA-DNA hybridization values in the genus Amycolatopsis and Amycolatopsis cynarae sp. nov., a novel actinobacterium from the rhizosphere soil of Cynara scolymus, and proposal of Amycolatopsis niigatensis as a synonym of Amycolatopsis echigonensis based on comparative genomic analysis

At present, it is widely believed that a 95-96% average nucleotide identity (ANI) value is equivalent to a 70% digital DNA-DNA hybridization (dDDH) value in the prokaryotic taxonomy. However, in the present study, comparative genome analysis of 29 pairs of Amycolatopsis type strains revealed that a 70% dDDH value did not correspond to a 95-96% ANI based on the MuMmer ultra-rapid aligning tool (ANIm) but approximately corresponded to a 96.6% ANIm value in the genus Amycolatopsis. Based on this corresponding relationship, phenotypic and chemotaxonomical characteristics, as well as phylogenetic analysis, an actinobacterial strain HUAS 11-8T isolated from the rhizosphere soil of Cynara scolymus, was subjected to a polyphasic taxonomic characterization. Based on EzBioCloud alignment, it was found that strain HUAS11-8T had the 16S rRNA gene similarities of 99.78% with A. rhizosphaerae JCM 32589T, 97.8% with A. dongchuanensis YIM 75904T, and < 97.8% sequence similarities to other Amycolatopsis species. Phylogenetic analysis of 16S rRNA gene sequences and whole-genome sequences revealed that strain HUAS 11-8T was closely related to A. rhizosphaerae JCM 32589T. ANIm and dDDH values between strains HUAS 11-8T and A. rhizosphaerae JCM 32589T were 96.3 and 68.5%, respectively, lower than the 96.6 and 70% thresholds recommended for the delineation of a novel Amycolatopsis species. Consequently, strain HUAS 11-8T should represent a novel Amycolatopsis species, for which the name Amycolatopsis cynarae sp. nov. (type strain HUAS 11-8T = MCCC 1K08337T = JCM 35980T) is proposed. Furthermore, based on comparative genomic analysis and rule 42 of the Prokaryotic Code, we propose that Amycolatopsis niigatensis is a later heterotypic synonym of Amycolatopsis echigonensis.

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).

Amycolatopsis anabasis sp. nov., a novel endophytic actinobacterium isolated from roots of Anabasis elatior

A novel endophytic actinobacterium, designated strain EGI 650086T, was isolated from the roots of Anabasis elatior (C.A.Mey.) Schischk. collected in Xinjiang, north-west China. The taxonomic position of the strain was investigated using a polyphasic taxonomic approach. Growth occurred at 15–40 °C, pH 6.0–8.0 and in the presence of 0–6 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequence and concatenation of 22 protein marker genes revealed that strain EGI 650086T formed a monophyletic clade within the genus Amycolatopsis and shared the highest sequence similarities with Amycolatopsis nigrescens JCM 14717T (97.1 %) and Amycolatopsis sacchari DSM 44468T (97.0 %). Sequence similarities with type strains of other species of the genus Amycolatopsis were less than 97.0 %. The average nucleotide identity and DNA–DNA hybridization values between strain EGI 650086T and the reference strains were 78.1–79.8 % and 22.1–23.0 %, respectively. The genome of strain EGI 650086T was 10.9 Mb, with a DNA G+C content of 70.1 mol%. The diagnostic diamino acid in the peptidoglycan was meso-diaminopimelic acid. The major whole-cell sugars contained arabinose, galactose, glucose and ribose. The predominant menaquinones were MK-9 (H4) and MK-9 (H2). Major fatty acids were iso-C16 : 0 and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The polar lipid profile of strain EGI 650086T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides, two unknown phospholipids, an unknown glycolipid and an unknown lipid. Polyphasic taxonomic characteristics indicated that strain EGI 650086T represents a novel species of the genus Amycolatopsis , for which the name Amycolatopsis anabasis sp. nov. is proposed. The type strain is EGI 650086T (=KCTC 49044T=CGMCC 4.7188T).

Amycolatopsis eburnea sp. nov., an actinomycete associated with arbuscular mycorrhizal fungal spores

A novel actinomycete, designated strain GLM-1^T, was isolated from arbuscular mycorrhizal fungal spores from Funneliformis mosseae RYA08, collected from Aquilaria crassna Pierre ex Lec. rhizosphere soil in Klaeng, Rayong Province, Thailand. Morphological characteristics of this strain included long chains of rod-like cells and squarish elements. The cell-wall composition of this novel isolate contained meso-diaminopimelic acid. The whole-cell diagnostic sugars were arabinose and galactose. The predominant menaquinone was MK-9(H₄). The major fatty acids were iso-C_16 : 0 and iso-C_15 : 0. Only phosphatidylethanolamine was detected as a polar lipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GLM-1^T was closely related to Amycolatopsis rhabdoformis SB026^T (99.11 %) with a low DNA-DNA hybridization value of 22.6-34.7 %. Genome sequencing revealed a genome size of 10 Mbp. There were obvious distinctions in the average nucleotide identity values between stain GLM-1^T and its closely related strains at around 86-93 % (ANIb) and 89-94 % (ANIm). The digital DNA-DNA hybridization values between strain GLM-1^T and type strains of phylogenetically related species were 34-55 %. The G+C content of the genomic DNA was 71.8 mol%. Based on these data, strain GLM-1^T is considered to represent a novel species of the genus Amycolatopsis, for which the name Amycolatopsiseburnea sp. nov. is proposed. The type strain is GLM-1^T (=TBRC 9315^T=NBRC 113658^T).

Pradimicin-IRD from Amycolatopsis sp. IRD-009 and its antimicrobial and cytotoxic activities

A new polycyclic antibiotic, pradimicin-IRD, was isolated from actinobacteria Amycolatopsis sp. IRD-009 recovered from soil of Brazilian rainforest undergoing restoration area. This molecule is the major compound produced in solid culture media. The new compound was detected by a focused method of precursor ion (high-performance liquid chromatography coupled to tandem mass spectrometer) developed previously to identify unusual aminoglycosyl sugar moieties. The compound was isolated and its structure was, therefore, elucidated by high-resolution mass spectrometry, and 1D and 2D nuclear magnetic resonance experiments. Pradimicin-IRD displayed potential antimicrobial activity against Streptococcus agalactiae (MIC 3.1 μg/mL), Pseudomonas aeruginosa (MIC 3.1 μg/mL) and Staphylococcus aureus (MIC 3.1 μg/mL), and also cytotoxicity against tumour and non-tumour cell lines with IC₅₀ values ranging from 0.8 μM in HCT-116 colon carcinoma cells to 2.7 μM in MM 200 melanoma cells. Particularly, these biological properties are described for the first time for this chemical class.

Transglutaminase from newly isolated Streptomyces sp. CBMAI 1617: Production optimization, characterization and evaluation in wheat protein and dough systems

The popularity of transglutaminase (TG) by the food industry and the variation in functionality of this enzyme from different origins, prompted us to isolate and evaluate a high-yielding TG strain. Through the statistical approaches, Plackett-Burman and response surface methodology, a low cost fermentation media was obtained to produce 6.074±0.019UmL^-1 of TG from a novel source; Streptomyces sp. CBMAI 1617 (SB6). Its potential exploitation was compared to commonly used TG, from Streptomyces mobaraensis. Biochemical and FT-IR studies indicated differences between SB6 and commercial TG (Biobond™ TG-M). Additions of TG to wheat protein and flour based doughs revealed that the dough stretching depended on the wheat protein fraction, TG amount and its origin. A higher degree of cross-linking of glutenins and of inclusion of gliadin in the polymers was seen for SB6 as compared to commercial TG. Thus, our results support the potential of SB6 to tailor wheat protein properties within various food applications.

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).

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

A novel member of the genus Amycolatopsis was isolated from soil collected from the banks of the Umgeni River, KwaZulu Natal province, South Africa. The strain, designated UM16(T), grouped with the type strains of Amycolatopsis alba, Amycolatopsis coloradensis and Amycolatopsis thailandensis by 16S rRNA gene based phylogeny. Genetic distance values, based on the gyrB and recN genes, between strain UM16(T) and its closest relatives were all above the threshold values of 0.02 and 0.04, respectively, that have been proposed to distinguish Amycolatopsis type strains. DNA-DNA hybridisation experiments confirmed that strain UM16(T) represents a unique genomic species, sharing 18.4 ± 5.1, 16.2 ± 1.8 and 45.8 ± 8.9 % DNA relatedness to the type strains of A. alba, A. coloradensis and A. thailandensis, respectively. The physiological, phylogenetic and DNA-relatedness data support the description of strain UM16(T) as the type strain of a novel species, for which the name Amycolatopsis umgeniensis sp. nov. is proposed (= DSM 45272(T) = NRRL B-24724(T)).

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 bacteriological nomenclature. 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.