The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

/pdf/genome-based-taxonomic-classification-of-the-phylum-4uc1zrzg88.pdf

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

New structurally diverse natural products are discovered when novel screening procedures are introduced or when high quality biological materials from new sources are examined in existing screens, hence it is important to foster these two aspects of novelty in drug discovery programmes. Amongst prokaryotes, actinomycetes, notably streptomycetes, remain a rich source of new natural products though it has become increasingly difficult to find such metabolites from common actinomycetes as screening ‘old friends’ leads to the costly rediscovery of known compounds. The bioprospecting strategy which is the subject of this review is based upon the premise that new secondary metabolites can be found by screening relatively small numbers of dereplicated, novel actinomycetes isolated from marine sediments. The success of the strategy is exemplified by the discovery of a range of novel bioactive compounds, notably atrop-abyssomicin C and proximicins A, B and C from Verrucosispora strains isolated from sediment samples taken from the Sea of Japan and the Raune Fjord, respectively, and the dermacozines derived from Dermacoccus strains isolated from the Challenger Deep of the Mariana Trench in the Pacific Ocean. The importance of current advances in prokaryotic systematics in work of this nature is stressed and a plea made that resources be sought to train, support and employ the next generation of actinobacterial systematists.

A guide to successful bioprospecting: Informed by actinobacterial systematics

Marine actinobacteria are the most economically as well as biotechnologically valuable prokaryotes. Representative genera of marine actinobacteria include Actinomadura, Aeromicrobium, Dietzia, Gordonia, Marinophilus, Micromonospora, Nonomuraea, Rhodococcus, Saccharomonospora, Saccharopolyspora, Salinispora, Streptomyces, Solwaraspora, Williamsia, Verrucosispora and several others. Among the genera of marine actinobacteria, the genus Streptomyces is represented in nature by the largest number of species and varieties, which differ greatly in their morphology, physiology, and biochemical activities. Marine Streptomyces occur in different biological sources such as fishes, molluscs, sponges, seaweeds and mangroves, besides seawater and sediments. In this review an evaluation is made on the present state of research on marine Streptomyces and its perspectives. The highlights include the production of metabolites such as antibiotics, anticancer compounds, enzymes, enzyme inhibitors and pigments by marine Streptomyces and their application as single cell protein and as probiotics in aquaculture. The marine environment contains a wide range of distinct Streptomyces that are not present in the terrestrial environment. With increasing advancement in science and technology, there would be greater demands in future for new bioactive compounds synthesised by Streptomyces from various marine sources.

Marine Streptomyces as a novel source of bioactive substances

A novel Streptomyces, strain MUSC 149T was isolated from mangrove soil. A polyphasic approach was used to study the taxonomy of MUSC 149T, which shows a range of phylogenetic and chemotaxonomic properties consistent with those of the members of the genus Streptomyces. The diamino acid of the cell wall peptidoglycan was LL-diaminopimelic acid. The predominant menaquinones were identified as MK9(H8) and MK9(H6). Phylogenetic analysis indicated that closely related strains include Streptomyces rhizophilus NBRC 108885T (99.2 % sequence similarity), Streptomyces gramineus NBRC 107863T (98.7 %) and Streptomyces graminisoli NBRC 108883T (98.5 %). The DNA–DNA relatedness values between MUSC 149T and closely related type strains ranged from 12.4 ± 3.3 % to 27.3 ± 1.9 %. The DNA G + C content was determined to be 72.7 mol%. The extract of MUSC 149T exhibited strong antioxidant activity and chemical analysis reported identification of an antioxidant agent, Pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro-. These data showed that metabolites of MUSC 149T shall be useful as preventive agent against free-radical associated diseases. Based on the polyphasic study of MUSC 149T, the strain merits assignment to a novel species, for which the name Streptomyces mangrovisoli sp. nov. is proposed. The type strain is MUSC 149T (= MCCC 1K00699T = DSM 100438T).

/pdf/presence-of-antioxidative-agent-pyrrolo-1-2-a-pyrazine-1-4-50bmdteugz.pdf

Presence of antioxidative agent, Pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro- in newly isolated Streptomyces mangrovisoli sp. nov.

Bacterial diseases in marine bivalves.

Actinomycete strain MCCC 1A01550(T), isolated from the national mangrove reserve in Fujian Province, China, was determined to belong to the genus Streptomyces based on a polyphasic approach. The cell wall of the novel strain contained ll-diaminopimelic acid and galactose. The predominant menaquinones were MK-9(H(4)) and MK-9(H(6)) and the major fatty acids were iso-C(16 : 0), cis9-C(16 : 1) and C(16 : 0). The diagnostic phospholipid was phosphatidylethanolamine. The DNA G+C content of the novel strain was 71.6 mol%. Phylogenetic analysis of 16S rRNA gene sequences confirmed the separation of the novel strain from recognized members of the genus Streptomyces available in public databases. DNA-DNA relatedness values between strain MCCC 1A01550(T) and the type strains of three related species ranged from 21.29 % to 43.38 %. Based on its phenotypic and genotypic characteristics, strain MCCC 1A01550(T) (=DSM 41903(T)=CGMCC 4.3534(T)) represents the type strain of a novel species, for which the name Streptomyces xiamenensis sp. nov. is proposed.

Streptomyces xiamenensis sp. nov., isolated from mangrove sediment

A novel isolate, designated strain MCCC 1A01535(T), belonging to the genus Streptomyces was isolated from the rhizosphere of the mangrove plant Avicennia mariana from Fujian Province, south China. Characterization of the isolate was based on a polyphasic approach. Pairwise comparison of 16S rRNA gene sequences revealed that strain MCCC 1A01535(T) shared 97.7 and 97.5 % sequence similarities to Streptomyces specialis GW41-1564(T) and Streptomyces hainanensis YIM47672(T), respectively, its most closely related neighbours, whereas the DNA-DNA relatedness value between strains MCCC 1A01535(T) and GW41-1564(T) was 50.2 %. The major fatty acids of strain MCCC 1A01535(T) were iso-C(16 : 0), C(16 : 0) and anteiso-C(15 : 0). These differed from the fatty acid compositions of related strains. Strain MCCC 1A01535(T) exhibited an unusual menaquinone system that comprised MK-10(H(6)) as the predominant component and moderate amounts of MK-9(H(6)), MK-9(H(8)) and MK-10(H(8)); minor amounts of MK-9(H(4)), MK-10(H(4)), MK-9(H(10)) and MK-10(H(10)) were also present. Based on its chemotaxonomic, phenotypic and genotypic characteristics, strain MCCC 1A01535(T) is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces avicenniae sp. nov. is proposed. The type strain is MCCC 1A01535(T) (=DSM 41943(T)=CGMCC 4.5510(T)).

Streptomyces avicenniae sp. nov., a novel actinomycete isolated from the rhizosphere of the mangrove plant Avicennia mariana

The taxonomic position of an actinomycete isolated from deep-sea sediment from the Indian Ocean was determined by using a polyphasic approach. The presence of iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0 as the major cellular fatty acids, ll-diaminopimelic acid as the characteristic diamino acid, and MK-9(H4, H6 and H8) as the major menaquinones supported the affiliation of strain IH32-1T to the genus Streptomyces. Comparison of 16S rRNA gene sequences showed that strain IH32-1T exhibited highest similarities to the type strains of Streptomyces globosus (97.6 %) and Streptomyces toxytricini (97.6 %). However, DNA–DNA relatedness values between strain IH32-1T and the type strains of S. globosus and S. toxytricini were determined as 55.2±4.7 and 38.3±2.5 %, respectively. Based on its chemotaxonomic, phenotypic and genotypic characteristics, strain IH32-1T is considered to represent a novel species in the genus Streptomyces, for which the name Streptomyces indicus sp. nov. is proposed. The type strain is IH32-1T ( = DSM 42001T = CGMCC 4.5727T).

Streptomyces indicus sp. nov., an actinomycete isolated from deep-sea sediment

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Streptomyces xiamenensis sp. nov., isolated from mangrove sediment

Streptomyces avicenniae sp. nov., a novel actinomycete isolated from the rhizosphere of the mangrove plant Avicennia mariana

Streptomyces indicus sp. nov., an actinomycete isolated from deep-sea sediment