Advanced prokaryotic systematics: the modern face of an ancient science

Prokaryotic systematics is one of the most progressive disciplines that has embraced technological advances over the last century. The availability and affordability of new sequencing technologies and user-friendly software have revolutionised the discovery of novel prokaryotic taxa, including the identification and nomenclature of uncultivable microorganisms. These advances have enabled scientists to resolve the structure of complex heterogenous taxon and to rectify taxonomic status of misclassified strains due to errors associated with the sensitivity and/or reproducibility of phenotypic approaches. Time- and labour-intensive experimental characterisation of strains could be replaced with determining the presence or absence of genes or operons responsible for phenotypic and chemotaxonomic properties, such as the presence of mycolic acids and menaquinones. However, the quality of genomic data must be acceptable and phylogenomic threshold values for interspecies and supraspecies delineation should be carefully considered in combination of genome-based phylogeny for a reliable and robust classification. These technological developments have empowered prokaryotic systematists to reliably identify novel taxa with an understanding of community ecology and their biosynthetic and biodegradation potentials

Permanent draft genome sequence of Frankia sp. NRRL B-16219 reveals the presence of canonical nod genes, which are highly homologous to those detected in Candidatus Frankia Dg1 genome

Frankia sp. NRRL B-16219 was directly isolated from a soil sample obtained from the rhizosphere of Ceanothus jepsonii growing in the USA. Its host plant range includes members of Elaeagnaceae species. Phylogenetically, strain NRRL B-16219 is closely related to “Frankia discariae” with a 16S rRNA gene similarity of 99.78%. Because of the lack of genetic tools for Frankia, our understanding of the bacterial signals involved during the plant infection process and the development of actinorhizal root nodules is very limited. Since the first three Frankia genomes were sequenced, additional genome sequences covering more diverse strains have helped provide insight into the depth of the pangenome and attempts to identify bacterial signaling molecules like the rhizobial canonical nod genes. The genome sequence of Frankia sp. strain NRRL B-16219 was generated and assembled into 289 contigs containing 8,032,739 bp with 71.7% GC content. Annotation of the genome identified 6211 protein-coding genes, 561 pseudogenes, 1758 hypothetical proteins and 53 RNA genes including 4 rRNA genes. The NRRL B-16219 draft genome contained genes homologous to the rhizobial common nodulation genes clustered in two areas. The first cluster contains nodACIJH genes whereas the second has nodAB and nodH genes in the upstream region. Phylogenetic analysis shows that Frankia nod genes are more deeply rooted than their sister groups from rhizobia. PCR-sequencing suggested the widespread occurrence of highly homologous nodA and nodB genes in microsymbionts of field collected Ceanothus americanus

Comparative Genomic Study of Vinyl Chloride Cluster and Description of Novel Species, Mycolicibacterium vinylchloridicum sp. nov.

Advanced physicochemical and chemical absorption methods for chlorinated ethenes are feasible but incur high costs and leave traces of pollutants on the site. Biodegradation of such pollutants by anaerobic or aerobic bacteria is emerging as a potential alternative. Several mycobacteria including Mycolicibacterium aurum L1, Mycolicibacterium chubuense NBB4, Mycolicibacterium rhodesiae JS60, Mycolicibacterium rhodesiae NBB3 and Mycolicibacterium smegmatis JS623 have previously been described as assimilators of vinyl chloride (VC). In this study, we compared nucleotide sequence of VC cluster and performed a taxogenomic evaluation of these mycobacterial species. The results showed that the complete VC cluster was acquired by horizontal gene transfer and not intrinsic to the genus Mycobacterium sensu lato. These results also revealed the presence of an additional xcbF1 gene that seems to be involved in Coenzyme M biosynthesis, which is ultimately used in the VC degradation pathway. Furthermore, we suggest for the first time that S/N-Oxide reductase encoding gene was involved in the dissociation of the SsuABC transporters from the organosulfur, which play a crucial role in the Coenzyme M biosynthesis. Based on genomic data, M. aurum L1, M. chubuense NBB4, M. rhodesiae JS60, M. rhodesiae NBB3 and M. smegmatis JS623 were misclassified and form a novel species within the genus Mycobacterium sensu lato. Mycolicibacterium aurum L1T (CECT 8761T = DSM 6695T) was the subject of polyphasic taxonomic studies and showed ANI and dDDH values of 84.7 and 28.5% with its close phylogenetic neighbour, M. sphagni ATCC 33027T. Phenotypic, chemotaxonomic and genomic data considering strain L1T (CECT 8761T = DSM 6695T) as a type strain of novel species with the proposed name, Mycolicibacterium vinylchloridicum sp. nov

Permanent Draft Genome Sequences of Three Frankia sp. Strains That Are Atypical, Noninfective, Ineffective Isolates

Here, we present draft genome sequences for three atypical Frankia strains (lineage 4) that were isolated from root nodules but are unable to reinfect actinorhizal plants. The genome sizes of Frankia sp. strains EUN1h, BMG5.36, and NRRL B16386 were 9.91, 11.20, and 9.43 Mbp, respectively

Permanent Draft Genome Sequence for Frankia sp. Strain Cc1.17, a Nitrogen-Fixing Actinobacterium Isolated from Root Nodules of Colletia cruciata

Frankia sp. strain Cc1.17 is a member of the Frankia lineage 3, the organisms of which are able to reinfect plants of the Eleagnaceae, Rhamnaceae, and Myricaceae families and the genera Gynmnostoma and Alnus. Here, we report the 8.4-Mbp draft genome sequence, with a G+C content of 72.14% and 6,721 candidate protein-coding genes

Streptomyces altiplanensis sp. Nov., an alkalitolerant species isolated from chilean altiplano soil, and emended description of streptomyces chryseus (krasil’nikov et al. 1965) pridham 1970

A polyphasic approach was used for evaluating the taxonomic status of strain HST21T isolated from Salar de Huasco in the Atacama Desert. The results of 16S rRNA gene and multilocus sequence phylogenetic analyses assigned strain HST21T to the genus Streptomyceswith Streptomyces albidochromogenes DSM 41800Tand Streptomyces flavidovirens DSM 40150T as its nearest neighbours. Digital DNA–DNA hydridization (dDDH) and average nucleotide identity (ANI) values between the genome sequences of strain HST21T and S. albidochromogenes DSM 41800T (35.6 and 88.2 %) and S. flavidovirens DSM 40105T (47.2 and 88.8 %) were below the thresholds of 70  and 95–96 % for prokaryotic conspecific assignation. Phenotypic, chemotaxonomic and genetic results distinguished strain HST21T from its closest neighbours. Strain HST21T is characterized by the presence of ll-diaminopimelic acid in its peptidoglycan layer; glucose and ribose as whole cell sugars; diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, glycophospholipids, unknown lipids and phospholipids as polar lipids; and anteiso-C15 : 0 (21.6 %) and anteiso-C17 : 0 (20.5 %) as major fatty acids (>15 %). Based on these results, strain HST21T merits recognition as a novel species, for which the name Streptomyces altiplanensis sp. nov. is proposed. The type strain is HST21T =DSM 107267T=CECT 9647T. While analysing the phylogenies of strain HST21T, Streptomyces chryseus DSM 40420T and Streptomyces helvaticus DSM 40431T were found to have 100 % 16S rRNA gene sequence similarity with digital DNA–DNA hydridization (dDDH) and average nucleotide identity (ANI) values of 95.3 and 99.4 %, respectively. Therefore, S. helvaticus is considered as a later heterotypic synonym of S. chryseus and, consequently, we emend the description of S. chryseus

Mycolicibacterium stellerae sp. nov., a rapidly growing scotochromogenic strain isolated from Stellera chamaejasme

A polyphasic study was undertaken to establish the taxonomic provenance of a rapidly growing Mycolicibacterium strain, CECT 8783T, recovered from the plant Stellera chamaejasme L. in Yunnan Province, China. Phylogenetic analyses based upon 16S rRNA and whole-genome sequences showed that the strain formed a distinct branch within the evolutionary radiation of the genus Mycolicibacterium . The strain was most closely related to Mycolicibacterium moriokaense DSM 44221T with 98.4 % 16S rRNA gene sequence similarity, but was distinguished readily from this taxon by a combination of chemotaxonomic and phenotypic features and by low average nucleotide identity and digital DNA–DNA hybridization values of 79.5 and 21.1 %, respectively. Consequently, the strain is considered, to represent a novel species of Mycolicibacterium for which the name Mycolicibacterium stellerae sp. nov is proposed; the type strain is I10A-01893T (=CECT 8783T=KCTC 19843T=DSM 45590T)

Streptomyces alkaliterrae sp. nov., isolated from an alkaline soil, and emended descriptions of Streptomyces alkaliphilus, Streptomyces calidiresistens and Streptomyces durbertensis

A polyphasic study was undertaken to establish the taxonomic position of six representative streptomycetes isolated from an alkaline soil adjacent to a meteoric alkaline soda lake in India. Chemotaxonomic, cultural and morphological properties of the isolates were consistent with their classification in the genus Streptomyces. The isolates formed extensively branched substrate mycelia and aerial hyphae that differentiated in straight chains of spores with smooth surfaces. They contained LL-diaminopimelic acid in the wall peptidoglycan, produced either hexa- or octa-hydrogenated menaquinones with nine isoprene units, major amounts of saturated, iso- and anteiso- fatty acids and phosphatidylethanolamine as the characteristic polar lipid. The isolates grew well at 30 °C, pH 9 and in the presence of 3 to 5% (w/v) sodium chloride. Isolates OF1T, OF3 and OF8 formed a distinct clade within the Streptomyces 16S rRNA gene tree sharing relatively high sequence similarities with the type strains of Streptomyces durbertensis (99.3%), Streptomyces palmae (98.1%) and Streptomyces xinghaiensis (98.3%), but can be distinguished from them using combinations of phenotypic properties. A phylogenomic tree based on draft genome sequences of the isolates and S. durbertensis DSM 104538T confirmed the phylogenetic relationships. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values calculated from the whole genome sequences of isolate OF1T and S. durbertensis DSM 104538T were low at 92.0% and 45.2%, respectively, indicating that they belong to different genomic species. Consequently, on the basis of the genomic, phylogenetic and associated phenotypic data it is proposed that isolates OF1T, OF3 and OF8 be assigned to the genus Streptomyces as Streptomyces alkaliterrae sp. nov. with strain OF1T (NCIMB 15195T =PCM 3001T) as the type strain. Isolates IF11, IF17 and IF19, and S. alkaliphilus DSM 42118T were shown to belong to the same taxospecies and together with S. calidiresistens DSM 42108T comprised a well supported clade in the Streptomyces 16S rRNA gene tree. Isolate IF17 and S. alkaliphilus DSM 42118T formed a well-supported clade in the phylogenomic tree, had almost identical digital G + C similarity values, produced long straight chains of smooth-surfaced spores and shared ANI and dDDH values (98.0 and 79.6%, respectively) consistent with their assignment to the same genomic species. In light of all of the data isolates IF11, IF17 and IF19 should be seen as authentic stains of S. alkalihilus. Data acquired in the present study have also been used to emend the descriptions of S. alkaliphilus, S. calidiresistens and S. durbertensis. The genomes of isolates IF17, and OF1T, OF3 and OF8 contain relatively high numbers of biosynthetic gene clusters some of which were discontinously distributed indicating ones predicted to express for novel specialised metabolites

Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation.

Nouioui I, Rückert C, Willemse J, et al. Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation. Antonie Van Leeuwenhoek. Journal of Microbiology. 2017;110(12):1705-1717.Two actinobacterial strains, ADI 127-17T and GBA 129-24, isolated from marine sponges Antho dichotoma and Geodia barretti, respectively, collected at the Trondheim fjord in Norway, were the subjects of a polyphasic study. According to their 16S rRNA gene sequences, the new isolates were preliminarily classified as belonging to the genus Actinoalloteichus. Both strains formed a distinct branch, closely related to the type strains of Actinoalloteichus hoggarensis and Actinoalloteichus hymeniacidonis, within the evolutionary radiation of the genus Actinoalloteichus in the 16S rRNA gene-based phylogenetic tree. Isolates ADI 127-17T and GBA 129-24 exhibited morphological, chemotaxonomic and genotypic features distinguishable from their close phylogenetic neighbours. Digital DNA: DNA hybridization and ANI values between strains ADI 127-17T and GBA 129-24 were 97.6 and 99.7%, respectively, whereas the corresponding values between both tested strains and type strains of their closely related phylogenetic neighbours, A. hoggarensis and A. hymeniacidonis, were well below the threshold for delineation of prokaryotic species. Therefore, strains ADI 127-17T (= DSM 46855T) and GBA 129-24 (= DSM 46856) are concluded to represent a novel species of the genus Actinoalloteichus for which the name of Actinoalloteichus fjordicus sp. nov. (type strain ADI 127-17T = DSM 46855T = CECT 9355T) is proposed. The complete genome sequences of the new strains were obtained and compared to that of A. hymeniacidonis DSM 45092T and A. hoggarensis DSM 45943T to unravel unique genome features and biosynthetic potential of the new isolates