Remember Me
Or use your Academic/Social account:


Or use your Academic/Social account:


You have just completed your registration at OpenAire.

Before you can login to the site, you will need to activate your account. An e-mail will be sent to you with the proper instructions.


Please note that this site is currently undergoing Beta testing.
Any new content you create is not guaranteed to be present to the final version of the site upon release.

Thank you for your patience,
OpenAire Dev Team.

Close This Message


Verify Password:
Verify E-mail:
*All Fields Are Required.
Please Verify You Are Human:
fbtwitterlinkedinvimeoflicker grey 14rssslideshare1
Idris, Hamidah; Labeda, David P.; Nouioui, Imen; Castro, Jean Franco; del Carmen Montero-Calasanz, Maria; Bull, Alan T.; Asenjo, Juan A.; Goodfellow, Michael (2017)
Publisher: Springer Nature
Journal: Antonie van Leeuwenhoek
Languages: English
Types: Article
Subjects: Molecular Biology, Q, Streptomyces, Atacama Desert, Aridus, Microbiology, Original Paper, Polyphasic taxonomy
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 material The online version of this article (doi:10.1007/s10482-017-0838-2) contains supplementary material, which is available to authorized users.
  • The results below are discovered through our pilot algorithms. Let us know how we are doing!

    • Antony-Babu S, Stach JEM, Goodfellow M (2010) Computerassisted numerical analysis of colour-group data for dereplication of streptomycetes for bioprospecting and ecological purposes. Antonie Van Leeuwenhoek 97:231-239. doi:10.1007/s10482-009-9404-x
    • Athalye M, Lacey J, Goodfellow M (1981) Selective isolation and enumeration of actinomycetes using rifampicin. J Appl Bacteriol 51:289-297. doi:10.1111/j.1365-2672.1981. tb01244.x
    • Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Klenk HP, Cle´ment C, Ouhdouch Y, van Wezel GP (2016) Taxonomy, physiology, and natural products of actinobacteria. Microbiol Mol Biol Rev 80:1-43. doi:10.1128/ mmbr.00019-15
    • Be´rdy J (2005) Bioactive microbial metabolites. J Antibiot 58:1-26
    • Bull AT (2011) Actinobacteria of the extremobiosphere. In: Horikoshi K (ed) Extremophiles Handbook. Springer, Tokyo, pp 1203-1240
    • Bull AT, Stach JEM (2007) Marine actinobacteria: new opportunities for natural product search and discovery. Trends Microbiol 15:491-499. doi:10.1016/j.tim.2007.10. 004
    • Bull AT, Asenjo JA, Goodfellow M, Go´mez-Silva B (2016) The Atacama Desert: technical resources and the growing importance of novel microbial diversity. Ann Rev Microbiol 70:215-234. doi:10.1146/annurev-micro-102215- 095236
    • Busarakam K (2014) Novel actinobacterial diversity in arid Atacama Desert soils as a source of new drug leads. PhD thesis, Newcastle University, UK
    • Busarakam K, Bull AT, Girard G, Labeda DP, van Wezel GP, Goodfellow M (2014) Streptomyces leeuwenhoekii sp. nov., the producer of chaxalactins and chaxamycins, forms a distinct branch in Streptomyces gene trees. Antonie Van Leeuwenhoek 105:849-861. doi:10.1007/s10482-014- 0139-y
    • Chaudhary HS, Soni B, Shrivastava AR, Shrivastava S (2013) Diversity and versatility of actinomycetes and its role in antibiotic production. J Appl PharmSc 3:S83-S94. doi:10. 7324/JAPS.2013.38.S14
    • Collins MD, Goodfellow M, Minnikin DE, Alderson G (1985) Menaquinone composition of mycolic acid-containing actinomycetes and some sporoactinomycetes. J Appl Bacteriol 58:77-86. doi:10.1111/j.1365-2672.1985.tb01431.x
    • Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and high-performance computing. Nat Methods 9:772. doi:10.1038/nmeth.2109
    • Demain A (2014) Importance of microbial natural products and the need to revitalize their discovery. J Ind Microbiol Biotechnol 41:185-201. doi:10.1007/s10295-013-1325-z
    • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
    • Gomez-Escribano JP, Castro JF, Razmilic V, Chandra G, Andrews BA, Asenjo JA, Bibb MJ (2015) The Streptomyces leeuwenhoekii genome: de novo sequencing and assembly in single contigs of the chromosome, circular plasmid pSLE1 and linear plasmid pSLE2. BMC Genom 16:1-11. doi:10.1186/s12864-015-1652-8
    • Goodfellow M (2013) Actinobacterial diversity as a sources of new drugs. Microbiologist 14:8-12
    • Goodfellow M, Fiedler HP (2010) A guide to successful bioprospecting: informed by actinobacterial systematics. Antonie Van Leeuwenhoek 98:119-142. doi:10.1007/ s10482-010-9460-2
    • Gu X, Fu YX, Li WH (1995) Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol 12:546-557
    • Guindon S, Dufayard J, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307-321. doi:10.1093/ sysbio/syq010
    • Hamedi J, Mohammadipanah F, Ventosa A (2013) Systematic and biotechnological aspects of halophilic and halotolerant actinomycetes. Extremophiles 17:1-13. doi:10.1007/ s00792-012-0493-5
    • Hong K, Gao A, Xie Q, Gao H, Zhuang L, Lin H, Yu H, Li J, Yao X, Goodfellow M, Ruan J (2009) Actinomycetes for marine drug discovery isolated from mangrove soils and plants in China. Mar Drugs 7:24-44
    • Idris H (2016) Actinobacterial diversity in Atacama Desert habitats as a road map to biodiscovery. PhD thesis, Newcastle University, UK
    • Isono K, Tyamashita S, Tomiyama Y, Suzuki S, Sakai H (1957) Studies on homomycin II. J Antibiotics (Tokyo) Series A 10:21-30
    • Jolley KA, Maiden MCJ (2010) BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinform 11:1-11. doi:10.1186/1471-2105-11-595
    • Ka¨mpfer P (2012) Genus Streptomyces. In: Goodfellow M, Ka¨mpfer P, Busse HJ, Trujillo ME, Suzuki K-i, Ludwig W, Whitman WB (eds) Bergey's manual of systematic bacteriology, vol 5. The Actinobacteria, vol 2. Springer, New York, pp 1455-1767
    • Ka¨mpfer P, Kroppenstedt RM, Dott W (1991) A numerical classification of the genera Streptomyces and Streptoverticillium using miniaturized physiological tests. J Gen Microbiol 137:1831-1891
    • Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772-780. doi:10. 1093/molbev/mst010
    • Kim SB, Goodfellow M (2002) Streptomyces thermospinisporus sp. nov., a moderately thermophilic carboxydotrophic streptomycete isolated from soil. Int J Syst Evol Microbiol 52:1225-1228. doi:10.1099/00207713-52-4-1225
    • Kim O, Cho Y, Lee K, Yoon S, Kim M, Na H, Park S, Jeon Y, Lee J, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716-721. doi:10.1099/ijs.0.038075-0
    • Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120
    • Kuykendall LD, Roy MA, O'Neill JJ, Devine TE (1988) Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Evol Microbiol 38:358-361. doi:10.1099/00207713-38-4- 358
    • Labeda DP (2011) Multi-locus sequence analysis of phytopathogenic species of Streptomyces. Int J Syst Evol Microbiol 61:2525-2531
    • Labeda DP (2016) Taxonomic evaluation of putative Streptomyces scabiei strains held in the ARS culture collection (NRRL) using multi-locus sequence analysis. Antonie Van Leeuwenhoek 109:349-356. doi:10.1007/s10482-015-0637-6
    • Labeda DP, Goodfellow M, Brown R, Ward AC, Lanoot B, Vanncanneyt M, Swings J, Kim SB, Liu Z, Chun J, Tamura T, Oguchi A, Kikuchi T, Kikuchi H, Nishii T, Tsuji K, Yamaguchi Y, Tase A, Takahashi M, Sakane T, Suzuki KI, Hatano K (2012) Phylogenetic study of the species within the family Streptomycetaceae. Antonie Van Leeuwenhoek 101:73-104. doi:10.1007/s10482-011-9656-0
    • Labeda DP, Doroghazi JR, Ju KS, Metcalf WW (2014) Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov. Int J Syst Evol Microbiol 64:894-900. doi:10.1099/ijs.0.058107-0
    • Labeda DP, Rong X, Huang Y, Doroghazi JR, Ju K-S, Metcalf WW (2016) Taxonomic evaluation of species of the Streptomyces hirsutus clade using multi-locus sequence analysis and proposals to reclarify several species in this clade. Int J Syst Evol Microbiol 66:2444-2450
    • Labeda DP, Dunlap CA, Rong X, Huang Y, Doroghazi JR, Ju K-S, Metcalf WW (2017) Phylogenetic relationships in the family Streptomy cetaceae using multi-locus sequence analysis Antonie van Leeuwenhoek (in press)
    • le Roes-Hill M, Meyers PR (2009) Streptomyces polyantibioticus sp. nov., isolated from the banks of a river. Int J Syst Evol Microbiol 59:1302-1309. doi:10.1099/ijs.0.006171-0
    • Lechevalier MP, Lechevalier HA (1970) Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Evol Microbiol 20:435-443. doi:10.1099/ 00207713-20-4-435
    • Miller LT (1982) Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 16:584-586
    • Minh BQ, Nguyen MAT, von Haeseler A (2013) Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol 30:1188-1195. doi:10.1093/molbev/mst024
    • Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233-241
    • Murray PR, Boron EJ, Pfaller MA, Tenover FC, Yolken RH (1999) Manual of Clinical Microbiology, 7th edn. ASM Press, Washington, DC
    • Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York
    • Nguyen L, Schmidt HA, von Haeseler A, Minh BQ (2015) IQTREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32:268-274. doi:10.1093/molbev/msu300
    • O'Donnell AG, Falconer C, Goodfellow M, Ward AC, Williams E (1993) Biosystematics and diversity amongst novel carboxydotrophic actinomycetes. Antonie Van Leeuwenhoek 64:325-340. doi:10.1007/BF00873091
    • Okoro CK, Brown R, Jones AL, Andrews BA, Asenjo JA, Goodfellow M, Bull AT (2009) Diversity of culturable actinomycetes in hyper-arid soils of the Atacama Desert, Chile. Antonie Van Leeuwenhoek 95:121-133. doi:10. 1007/s10482-008-9295-2
    • Rong X, Huang Y (2012) Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA-DNA hybridization, validating the MLSA scheme for systematics of the whole genus. Syst Appl Microbiol 35:7-18. doi:10.1016/j.syapm.2011.10. 004
    • Rong X, Huang Y (2014) Multi-locus sequence analysis: taking prokaryotic systematics to the next level. Methods Microbiol 41:221-251. doi:10.1016/bs.mim.2014.10.001
    • Sasser MJ (1990) Identification of bacteria by gas chromatography of cellular fatty acids. Del: Microbial ID Inc, Newark
    • Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Evol Microbiol 16:313-340
    • Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226-231
    • Suguwara R, Onuma M (1957) Melanomycin, a new antitumor substance from Streptomyces. II. Description of strain. J Antibiotics (Tokyo) 10:138-142
    • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725-2729
    • Tiwari K, Gupta RK (2012) Rare actinomycetes: a potential storehouse for novel antibiotics. Crit Rev Biotech 32:108-132. doi:10.3109/07388551.2011.562482
    • Vaas LAI, Sikorski J, Michael V, Go¨ker M, Klenk HP (2012) Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS ONE 7:e34846. doi:10.1371/journal.pone.0034846
    • Vaas LAI, Sikorski J, Hofner B, Fiebig A, Buddruhs N, Klenk HP, Go¨ker M (2013) opm: an R package for analysing OmniLog phenotype microarray data. Bioinformatics. doi:10.1093/bioinformatics/btt291
    • Waksman SA, Henrici AT (1943) The nomenclature and classification of the actinomycetes. J Bacteriol 46:337-341
    • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Tru¨per HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463-464. doi:10. 1099/00207713-37-4-463
    • Wellington EMH, Stackebrandt E, Sanders D, Wolstrup J, Jorgensen NO (1992) Taxonomic status of Kitasatospora, and proposed unification with Streptomyces on the basis of phenotypic and 16S rRNA analysis and emendation of Streptomyces Waksman and Henrici 1943, 339AL. Int J Syst Bacteriol 42:156-160
    • Williams ST, Goodfellow M, Alderson G, Wellington EMH, Sneath PHA, Sackin MJ (1983) Numerical classification of Streptomyces and related genera. J Gen Microbiol 129:1743-1813
    • Witt D, Stackebrandt E (1990) Unification of the genera Streptoverticillum and Streptomyces, and emendation of Streptomyces Waksman and Henrici 1943, 339AL. Syst Appl Microbiol 13:361-371
  • Inferred research data

    The results below are discovered through our pilot algorithms. Let us know how we are doing!

    Title Trust
  • No similar publications.

Share - Bookmark

Cite this article