A guide to successful bioprospecting: informed by actinobacterial systematics
Tóm tắt
Từ khóa
Tài liệu tham khảo
Abdel-Mageed WM, Milne BF, Wagner M, Schumacher M, Sandor P, Pathom-aree W, Goodfellow, Bull AT, Horikoshi K, Ebel R, Diedrich M, Fiedler H-P, Jaspars M (2010) Dermacozines, a new phenazine family from deep-sea dermacocci isolated from a Mariana Trench sediment. Org Biomol Chem 8:2352–2362
Achtman M, Wagner M (2008) Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 6:431–440
Allgaier M, Grossart H-P (2006) Diversity and seasonal dynamics of Actinobacteria populations in four lakes in Northeastern Germany. Appl Environ Microbiol 72:3489–3497
Antony-Babu S, Goodfellow M (2008) Biosystematics of alkaliphilic streptomycetes isolated from seven locations across a beach and dune sand system. Antonie van Leeuwenhoek 94:581–591
Antony-Babu S, Stach JEM, Goodfellow M (2008) Genetic and phenotypic evidence for Streptomyces griseus ecovars isolated from a beach and dune sand system. Antonie van Leeeuwenhoek 94:63–74
Antony-Babu S, Stach JEM, Goodfellow M (2010) Computer-assisted numerical analysis of colour group data for dereplication of streptomycetes for bioprospecting and ecological purposes. Antonie van Leeuwenhoek 97:231–239
Asolkar RN, Freel KC, Jensen PR, Fenical W, Kondratyuk ParkE-J, Pezzuto JM (2009) Arenamides A-C, cytotoxic NFkB inhibitors from the marine actinomycete Salinispora arenicola. J Nat Prod 72:396–402
Atalan E, Manfio GP, Ward AC, Kroppenstedt RM, Goodfellow M (2000) Biosystematic studies on novel streptomycetes from soil. Antonie van Leeuwenhoek 77:337–353
Athalye M, Lacey J, Goodfellow M (1981) Selective isolation and enumeration of actinomycetes using rifampicin. J Appl Microbiol 51:289–291
Baltz RH (2005) Antibiotic discovery from actinomycetes: will a renaissance follow the decline and fall? SIM News 55:186–196
Baltz RH (2008) Renaissance in antibacterial discovery from actinomycetes. Curr Opin Pharmacol 8:557–563
Bentley SD, Cerdano-Tarraga AM, Challis GL et al (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141–147
Bister B, Bischoff D, Ströbele M, Riedlinger J, Reicke A, Wolter F, Bull AT, Zähner H, Fiedler H-P, Süssmuth RD (2004) Abyssomicin C—a polycyclic antibiotic from a marine Verrucosispora strain as an inhibitor of the p-aminobenzoic acid/tetrahydrofolate biosynthesis pathway. Angew Chem Int Ed 43:2574–2576
Bousfield IJ (1993) Bacterial nomenclature and its role in systematics. In: Goodfellow M, O’Donnell AG (eds) Handbook of new bacterial systematics. Academic Press, London, pp 317–338
Brandão PFB, Torimura M, Kurane R, Bull AT (2002) Dereplication for biotechnology screening: PyMS and PCR-RFLP-SSCP (PRS) profiling of 16S rRNA genes of marine and terrestrial actinomycetes. Appl Microbiol Biotechnol 58:77–83
Bredholdt H, Galatenko OA, Engelhardt K, Tjaervik E, Terekhova LP, Zotchev SB (2007) Rare actinomycete bacteria from the shallow water sediments of the Trondheim fjord, Norway: isolation, diversity and biological activity. Environ Microbiol 9:2756–2764
Bredholdt H, Tjaervik E, Johnsen G, Zotchev SB (2008) Actinomycetes from sediments in the Trondheim fjord, Norway: diversity and biological activity. Mar Drugs 6:12–24
Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) (2005) Bergey’s manual of systematic bacteriology, 2nd edn, vol 2, part A, introductory essays. Springer, USA, pp 1–304
Bull AT (2004a) Biotechnology, the art of exploiting biology. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM Press, Washington, pp 3–12
Bull AT (2004b) The paradigm shift in microbial prospecting. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM Press, Washington, pp 241–249
Bull AT (2010) Actinobacteria of the extremobiosphere. In: Horikoshi K, Antranikian G, Bull AT, Robb F, Stelter K (eds) Extremophiles handbook. Springer-Verlag GmbH, Berlin (in press)
Bull AT, Stach JEM (2007) Marine actinobacteria: new opportunities for natural product search and discovery. Trends Microbiol 15:491–499
Bull AT, Ward AC, Goodfellow M (2000) Search and discovery strategies for biotechnology: the paradigm shift. Microbiol Mol Biol Rev 64:573–606
Bull AT, Stach JEM, Ward AC, Goodfellow M (2005) Marine actinobacteria; perspectives, challenges, future directions. Antonie van Leeuwenhoek 87:65–79
Chen Y-G, Wang Y-X, Zhang Y-Q, Tang S-K, Liu Z-X, Xioa H-D, Xu L-H, Cui X-L, Li W-J (2009) Nocardiopsis litoralis sp. nov., a halophilic marine actinomycete isolated from a sea anemone. Int J Syst Evol Microbiol 59:2708–2713
Coleman ML, Sullivan MB, Martiny AC, Barry K, Delong EF, Chisholm SW (2006) Genomic islands and the ecology and evolution of Prochlorococcus. Science 311:1768–1770
Colquhoun JA, Mexson J, Goodfellow M, Ward AC, Horikoshi K, Bull AT (1998) Novel rhodococci and other mycolate actinomycetes from the deep sea. Antonie van Leeuwenhoek 74:27–40
Colwell RR (1970) Polyphasic taxonomy of bacteria. In: Iizaka H, Hasegawa T (eds) Culture collections of microorganisms. University of Tokyo Press, Tokyo, pp 421–436
Czaran TL, Hoekstra RE, Page L (2002) Chemical warfare between microbes promotes biodiversity. Proc Natl Acad Sci USA 99:786–790
Dai H-Q, Wang J, Xim Y-H, Pei G, Tang S-K, Ren B, Ward A, Ruan J-S, Li W-J, Zhang L-X (2010). Verrucosispora sediminis sp. nov., a novel cyclodipeptide producing actinomycete from the South China Sea. Int J Syst Evol Microbiol. doi: 10.1099/ijs.0.017053-0
De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer K-H, Whitman WB (eds) (2009) Bergey’s manual of systematic bacteriology, 2nd edn, vol 3, The Firmicutes. Springer, USA, pp 1–1450
Drautz H, Keller-Schierlein W, Zähner H (1975) Lysolipin I, ein neues Antibiotikum aus Streptomyces violaceoniger. Arch Microbiol 106:175–190
Duangmal K, Ward AC, Goodfellow M (2005) Selective isolation of members of the Streptomyces violaceoruber clade from soil. FEMS Microbiol Lett 243:321–327
Epstein, Lewis K, Nichols D, Gavrish E (2010) New approaches to microbial isolation. In: Manual of industrial microbiology and biotechnology, 3rd edn. Baltz RH, Davies J, Demain AL (volume eds) Section 1: Isolation and screening for secondary metabolites and enzymes, Bull AT, Davies JE (section eds). ASM Press, Washington, DC, pp 3–12
Feling RH, Buchanan GO, Mincer TJ, Kauffman CA, Jensen PR, Fenical W (2003) Salinosporamide A: a high cytotoxic proteasome inhibitor from a novel microbial source, a marine bacterium of the new genus Salinospora. Angew Chem Int Ed 42:355–357
Felis GE, Torriani S, van Hylckama Vlieg JT, Oren A (2010) Taxonomic characterization of prokaryotic microorganisms. In: Manual of industrial microbiology and biotechnology, 3rd edn. Baltz RH, Davies J, Dermain AL (volume eds) Section 1: Isolation and screening of secondary metabolites and enzymes, Bull AT, Davies J (section eds). ASM Press, Washington, DC, pp 28–42
Fenical W, Jensen PR (2006) Developing a new resource for drug discovery: marine actinomycete bacteria. Nat Chem Biol 2:666–673
Fenical W, Jensen PR, Palladino MA, Lam KS, Lloyd GK, Potts BC (2009) Discovery and development of the anticancer agent salinosporamide A (NPI-0052). Biorg Med Chem 17:2175–2180
Ferguson EV, Ward AC, Sanglier J-J, Goodfellow M (1997) Evaluation of Streptomyces species-groups by pyrolysis mass spectrometry. Zbl Bakt 285:169–181
Fiedler H-P (1993) Biosynthetic capacities of actinomycetes. 1. Screening for secondary metabolites by HPLC and UV-visible absorbance spectral libraries. Nat Prod Lett 2:119–128
Fiedler H-P (1994) Biosynthetic capacities of actinomycetes. 2. Juglomycin Z, a new naphthoquinone antibiotic from Streptomyces tendae. J Antibiot 47:1116–1122
Fiedler H-P (2010) Secondary metabolites isolated by the Fiedler group. http://www.mikrobio.uni-tuebingen.de/ag_fiedler/index.php
Fiedler H-P, Bruntner C, Bull AT, Ward AC, Goodfellow M, Potterat O, Puder C, Mihm M (2005) Marine actinomycetes as a source of novel secondary metabolites. Antonie van Leeuwenhoek 87:37–42
Fiedler H-P, Bruntner C, Riedlinger J, Bull AT, Knutsen G, Goodfellow M, Jones AL, Maldonado L, Pathom-aree W, Beil W, Schneider K, Keller S, Süssmuth RD (2008) Proximicin A, B and C, novel aminofuran antibiotic and anticancer compounds isolated from marine strains of the actinomycete Verrucosispora. J Antibiot 61:158–163
Frisvad JC (2010) Metabolonics for the discovery of novel compounds. In: Manual of industrial microbiology and biotechnology, 3rd edn. Baltz RH, Davies J, Demain AL (volume eds) Section 1: Isolation and screening of secondary metabolites and enzymes, Bull AT, Davies JE (section eds). ASM Press, Washington, DC, pp 73–77
Frisvad JC, Andersen B, Thrane U (2008) The use of secondary metabolite profiling in chemotaxonomy of filamentous fungi. Mycol Res 112:231–240
Fry JS (2004) Culture dependent microbiology. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM Press, Washington, DC, pp 80–91
Gao B, Gupta RS (2005) Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria. Int J Syst Evol Microbiol 55:2401–2412
Gao B, Paramanathan B, Gupta RS (2006) Signature proteins that are characteristic of Actinobacteria and their subgroups. Antonie van Leeuwenhoek 90:69–91
Gillis M, Vandamme P, De Vos P, Swings J, Kersters K (2005) Polyphasic taxonomy. In: Brenner DJ, Krieg R, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology, 2nd edn, vol 2, the proteobacteria, part A, introductory essays. Springer, USA, pp 43–48
Giovanonni SJ, Stingl U (2005) Molecular diversity and ecology of microbial plankton. Nature 437:343–348
Gontang EA, Fenical W, Jensen PR (2007) Phylogenetic diversity of Gram-positive bacteria cultured from marine sediments. Appl Environ Microbiol 73:3272–3282
Goodfellow M (2010) Selective isolation of actinobacteria. In: Manual of industrial microbiology and biotechnology, 3rd edn. Baltz RH, Davies J, Demain AL (volume eds) Section 1: Isolation and screening of secondary metabolites and enzymes, Bull AT, Davies JE (section eds). ASM Press, Washington, DC, pp 13–27
Goodfellow M, Cross T (1984) Classification. In: Goodfellow M, Mordarski M, Williams ST (eds) The biology of the actinomycetes. Academic Press, London, pp 7–164
Goodfellow M, Haynes JA (1984) Actinomycetes in marine sediments. In: Ortiz-Ortiz L, Bojalil LF, Yakoleff V (eds) Biological, biochemical and biomedical aspects of actinomycetes. Academic Press, Orlando, pp 453–472
Goodfellow M, Maldonado LA (2006) The families Dietziaceae, Gordoniaceae, Nocardiaceae and Tsukamurellaceae. In: Dworkin M, Falkow S, Schleifer KH, Stackebrandt E (eds) The prokaryotes, 3rd edn, vol 3, Archaea and Bacteria: Firmicutes, Actinomycetes. Springer, New York, pp 843–888
Goodfellow M, Manfio GP, Chun J (1997) Towards a practical species concept for cultivable bacteria. In: Claridge MF, Dawah HA, Wilson MR (eds) Species, the units of diversity. Chapman and Hall, London, pp 25–59
Goodfellow M, Kumar Y, Labeda DP, Sembiring L (2007) The Streptomyces violaceusniger clade: a home for streptomycetes with rugose ornamented spores. Antonie van Leeuwenhoek 92:173–199
Goodfellow M, Maldonado LA, Jones AL, Mexson J, Fiedler H-P, Stach JEM, Bull AT (2010a) Verrucosispora maris sp. nov., a novel actinomycete isolated from a marine sediment which produces abyssomicins. Int J Syst Evol Microbiol (in press)
Goodfellow M, Kämpfer P, Busse HJ, Trujillo M, Suzuki K-E, Ludwig W, Whitman WB (2010b) Bergey’s manual of systematic bacteriology, 2nd edn, vol 3, The Actinobacteria. Springer, USA (in press)
Graf E, Schneider K, Nicholson G, Ströbele M, Jones AL, Goodfellow M, Beil W, Süssmuth D, Fiedler HP (2007) Elloxazinones A and B, new aminophenoxazinones from Streptomyces griseus ACTA 2871. J Antibiot 60:277–284
Guo Y, Zhang W, Rong X, Huang Y (2008) A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics. Int J Syst Evol Microbiol 58:149–159
Gupta RS (2009) Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades. Int J Syst Ecol Microbiol 59:2510–2526
Hahn MW (2009) Description of seven candidate species affiliated with the phylum Actinobacteria, representing planktonic freshwater bacteria. Int J Syst Evol Microbiol 59:112–117
Hamada M, Iino T, Iwami T, Tamura T, Harayama S, Suzuki K-I (2009) Arsenicococcus piscis sp. nov., a mesophilic actinobacterium isolated from the intestinal tract of a fish. Actinomycetologia 23:40–45
Han SK, Nedashkviskaya OI, Mikhailov VV, Kim SB, Bae KS (2003) Salinibacterium amurskyyense gen. nov., sp. nov., a novel genus of the family Microbacteriaceae from the marine environment. Int J Syst Evol Microbiol 53:2061–2066
Handelsman J (2004) Soils—the metagenomics approach. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM Press, Washington, pp 109–119
Hayakawa M, Nonomura H (1987) Humic acid-vitamins agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 65:501–509
Hohmann C, Schneider K, Bruntner C, Brown R, Jones AL, Goodfellow M, Kramer M, Imhoff JF, Nicholson G, Fiedler H-P, Süssmuth RD (2009a) Albidopyrone, a new α-pyrone-containing metabolite from marine-derived Streptomyces sp. NTK 227. J Antibiot 62:75–79
Hohmann C, Schneider K, Bruntner C, Irran E, Nicholson G, Bull AT, Jones AL, Brown R, Stach JEM, Goodfellow M, Beil W, Krämer M, Imhoff JF, Süssmuth RD, Fiedler H-P (2009b) Caboxamycin, a new antibiotic of the benzoxazole family and phosphodiesterase inhibitor, produced by the deep-sea strain Streptomyces sp. NTK 937. J Antibiot 62:99–104
Hong K, Gao A-H, Xie Q-Y, Gao H, Zhuang L, Lin H-P, Yu H-P, Yao X-S, Goodfellow M, Ruan J-S (2009) Actinomycetes for marine drug discovery isolated from mangrove soils and plants in China. Mar Drugs 7:24–44
Hopkins DW, MacNaughton SJ, O’Donnell AG (1991) A dispersion and differential centrifugation technique for representative sampling microorganisms from soil. Soil Biol Biochem 23:217–225
House of Lords, Science and Technology Committee 5th Report (2007–2008) Systematics and taxonomy: follow-up. The Stationary Office Limited, London, pp 1–330
Hozzein WN, Goodfellow M (2007) Nonomuraea aegyptia sp. nov., a novel actinomycete isolated from a sand dune. Antonie van Leeuwenhoek 92:165–171
Huber L, Fiedler H-P (1991) HPLC with computerized diode array detection in pharmaceutical research. In: Fong GW, Lam SK (eds) HPLC in the pharmaceutical industry. Marcel Dekker, New York, pp 123–146
Ikeda H, Ishikawa J, Hanamoto A, Shinose H, Kikuchi T, Shiba Y, Sakoki Y, Hattori M, Ōmura S (2003) Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat Biotechnol 21:526–531
Jensen PR (2010) Linking species concepts to natural product discovery in the post-genomic era. J Ind Microbiol Biotechnol 37:219–224
Jensen PR, Lauro FM (2008) An assessment of actinobacterial diversity in the marine environment. Antonie van Leeuwenhoek 94:51–62
Jensen PR, Mafnas C (2006) Biogeography of the marine actinomycete Salinispora. Environ Microbiol 8:1881–1888
Jensen PR, Dwight R, Fenical W (1991) Distribution of actinomycetes in near-shore tropical marine sediments. Appl Microbiol 57:1102–1108
Jensen PR, Gontang E, Mafnas C, Mincer TJ, Fenical W (2005a) Culturable marine actinomycete diversity from tropical Pacific Ocean sediments. Environ Microbiol 7:1039–1048
Jensen PR, Mincer TJ, Williams PG, Fenical W (2005b) Marine actinomycete diversity and natural product discovery. Antonie van Leeuwenhoek 87:43–48
Jensen PR, Williams PG, Oh CD, Zeigker L, Fenical W (2007) Species specific secondary metabolite production in marine actinomycetes of the genus Salinispora. Appl Environ Microbiol 73:1146–1152
Jiang S, Sun W, Chen M, Dai S, Zhang L, Liu Y, Lee KJ, Li X (2007) Diversity of culturable actinobacteria isolated from marine sponge Haliclona sp. Antonie van Leeuwenhoek 92:405–416
Keller S, Nicholson G, Drahl C, Sorensen E, Fiedler H-P, Süssmuth RD (2007a) Abyssomicins G and H and atrop-abyssomicin C from the marine Verrucosispora strain AB-18-032. J Antibiot 60:391–394
Keller S, Schadt HS, Ortel I, Süssmuth RD (2007b) Action of atrop-abyssomicin C as an inhibitor of 4-amino-4-deoxychorismate synthease PabB. Angew Chem Int Ed 46:8284–8286
Khan ST, Harayama S, Tamura T, Ando K, Takagi M, Kazuo S-Y (2009) Paraoerskovia marina gen. nov., sp. nov., an actinobacterium isolated from marine sediment. Int J Syst Evol Microbiol 59:2094–2098
Khan ST, Tamura T, Takagi M, Shin-Ya K (2010) Streptomyces tatejamensis sp. nov., Streptomyces marinus sp. nov. and Streptomyces haliclonae sp. nov., three novel species of Streptomyces isolated from marine sponge Haliclona sp. Int J Syst Evol Microbiol. doi: 10.1099/ijs.0.019869-0
Kim BS, Oh HN, Kang H, Park SS, Chun J (2004) Remarkable bacterial diversity in the tidal flat sediment as revealed by 16S rRNA analysis. J Microbiol Biotechnol 14:205–211
Kim TK, Garson MJ, Fuerst JA (2005) Marine actinomycetes related to the “Salinispora” group from the Great Barrier Reef sponge Pseudoceratina clavata. Environ Microbiol 7:509–519
Kim B-Y, Stach JEM, Weon H-Y, Kwon S-W, Goodfellow M (2010) Three new species of Dactylsporangium isolated from soil: Dactylosporangium luridium sp. nov., Dactylosporangium luteum sp. nov. and Dactylosporangium salmoneum sp. nov. Int J Syst Evol Microbiol. doi: 10.1099/ijs.0.016451-0
Koeppel A, Perry EB, Sckorski J, Krizane D, Warner A et al (2008) Identifying the fundamental units of bacterial diversity, a paradigm shift to incorporate ecology into bacterial systematics. Proc Natl Acad Sci USA 105:2504–2509
Konstantinidis KT, Tiedje JM (2005) Genomic insights into the species definition for prokaryotes. Proc Natl Acad Sci USA 102:2567–2572
Konstantinidis KT, Tiedje JM (2007) Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 10:504–509
Kopke B, Wilins R, Engelen B, Cypionka H, Sass H (2005) Microbial diversity in coastal subsurface sediments: a cultivation approach using various electron acceptors and substrate gradients. Appl Environ Microbiol 71:7819–7830
Krieg NR (2005) Identification of prokaryotes. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology, 2nd edn, vol 2, part A, introductory essays. Springer, USA, pp 33–38
Kroppenstedt RM, Goodfellow M (2006) The family Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillispora and Thermomonospora. In: Dworkin M, Falkow S, Schleifer KH, Stackebrandt E (eds) The prokaryotes, 3rd edn, vol 3, Archaea and Bacteria: Firmicutes, Actinomycetes. Springer, New York, pp 682–724
Kumar Y, Goodfellow M (2008) Five new members of the Streptomyces violaceusniger 16S rRNA gene clade: Streptomyces castelarensis comb. nov., S. humastatinus sp. nov., S. mordarskii sp. nov., S. rapamycinicus sp. nov. and S. ruanii sp. nov. Int J Syst Microbiol 58:1369–1378
Kumar Y, Goodfellow M (2010) Reclassification of Streptomyces hygroscopicus strains as Streptomyces aldersoniae sp. nov., Streptomyces augustmycinicus sp. nov., comb. nov. Streptomyces ascomycinicus sp. nov., Streptomyces decoyicus sp. nov., comb. nov., Streptomyces milbemycinicus sp. nov. and Streptomyces wellingtoniae sp. nov. Int J Syst Ecol Microbiol 60:769–775
Kumar Y, Aiemsun-ang P, Ward AC, Goodfellow M (2007) Diversity and geographical distribution of members of the Streptomyces violaceusniger 16S rRNA gene clade detected by clade specific primers. FEMS Microbiol Ecol 62:54–63
Kunisawa T (2007) Gene arrangements characteristic of the phylum Actinobacteria. Antonie van Leeuwenhoek 92:359–365
Kunst F, Ogasawara N, Mosyer I, Albertini AM, Alloni V et al (1997) The complete sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390:249–256
Kurahashi M, Tukanaga Y, Sakiyama Y, Harayama S, Yokota A (2009) Iamia majanohamensis gen. nov., sp. nov., an actinobacterium isolated from sea cucumber Holothuria edulis, and proposal of Iamiaceae fam nov. Int J Syst Evol Microbiol 59:869–873
Kurahashi M, Tukunaga Y, Sakiyama Y, Harayama S, Yokota A (2010) Euzebya tangerine gen. nov., a deeply branching actinobacterium isolated from the sea cucumber Halothuria edulis and proposal of Euzebyaceae fam. nov., Euzebyales ord. nov. and Nitriliruptoridae subclassis nov. Int J Syst Evol Microbiol. doi: 10.1099/ijs.0.016543-0
Lam KS (2006) Discovery of novel metabolites from marine actinomycetes. Curr Opin Microbiol 9:245–251
Lapage SP, Sneath PHA, Lessel EF, Skerman VBD, Seeliger HPR, Clark WA (eds) (1975) International code of nomenclature of bacteria, 1975 revision. American Society for Microbiology, Washington, DC
Lapage SP, Sneath PHA, Lessel EF Jr, Skerman VBD, Seeliger HPR, Clark WA (eds) (1992) International code of nomenclature of bacteria (1990) revision: bacteriological code. American Society for Microbiology, Washington, DC
Larsen TO, Smedsgaard J, Nielson KF, Hansen ME, Frisvad JC (2005) Phenotypic taxonomy and metabolite profiling in microbial drug discovery. Nat Prod Rep 22:672–695
Lee SD (2008) Phycicococcus jejuensis gen. nov., sp. nov., an actinomycete isolated from seaweed. Int J Syst Evol Microbiol 56:2369–2373
Lee DW, Lee JM, Seo JP, Schumann P, Kim SJ, Lee SD (2008) Phycicola gilvas gen. nov., sp. nov., an actinobacterium isolated from living seaweed. Int J Syst Evol Microbiol 58:1318–1323
Li Hr, Yu Y, Luo W, Zeng Y-X (2010) Marisediminicola antarctica gen. nov., sp. nov., an actinobacterium isolated from the Antarctic. Int J Syst Evol Microbiol. doi: 10.1099/ijs.0.018754-0
Liao Z-L, Tang S-K, Guo L, Zhang y-Q, Tian X-P, Jian C-L, Xu L-H, Li WJ (2009) Vewrrucosispora lutea sp. nov., isolated from a mangrove sediment sample. Int J Syst Evol Microbiol 59:2129–2379
Liu Z, Li Y, Zheng L-Q, Huang Y-J, Li W-J (2010) Saccharomonospora marina sp. nov., isolated from an ocean sediment in the East China Sea. Int J Syst Evol Microbiol. doi: 10.1099/ijs.0.017038-0
Ludwig W, Klenk H-P (2005) Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systematics. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology, 2nd edn, vol 2, the proteobacteria, part A, introductory essays. Springer, USA, pp 49–65
MacNaughton SJ, O’Donnell AG (1994) Tuberculostearic acid as a means of estimating the recovery (using dispersion and differential centrifugation) of actinomycetes from soil. J Microbiol Methods 20:69–77
Magarvey NA, Keller JM, Bernan V, Dworkin M, Skerman DH (2004) Isolation and characterization of novel marine-derived actinomycete taxa rich in bioactive metabolites. Appl Environ Microbiol 70:7520–7529
Maldonado LA, Stach JEM, Pathom-aree W, Ward AC, Bull AT, Goodfellow M (2005a) Diversity of cultivable actinobacteria in geographically widespread marine sediments. Antonie van Leeuwenhoek 87:11–18
Maldonado LA, Fenical W, Jensen PR, Kauffman CA, Mincer TJ, Ward AC, Bull AT, Goodfellow M (2005b) Salinispora arenicola gen. nov., sp. nov. and Salinispora tropica sp. nov., obligate marine actinomycetes belonging to the family Micromonosporaceae. Int J Syst Evol Microbiol 55:1759–1766
Maldonado LA, Stach JEM, Ward AC, Bull AT, Goodfellow M (2008) Characterisation of micromonosporae from aquatic environments using molecular taxonomic methods. Antonie van Leeuwenhoek 94:289–298
Maldonado LA, Frangoso-Yáñez D, Pérez-Garciä A, Rosellón-Druker J, Quintana E (2009) Actinobacterial diversity from marine sediments collected in Mexico. Antonie van Leeuwenhoek 95:111–120
Manfio GP, Atalan E, Zakrzewska-Czerwinska J, Mordarski M, Rodriguez C, Collins MD, Goodfellow M (2003) Classification of novel soil streptomycetes as Streptomyces aureus sp. nov., Streptomyces laceyi sp. nov. and Streptomyces sanglieri sp. nov. Antonie van Leeuwenhoek 83:245–255
McLeod MP, Warren H, Hsiao WW, Araki N, Myhre M et al (2006) The complete genome of Rhodococcus RHA 1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci 103:15582–15587
McVeigh HP, Munro J, Embley TM (1996) Molecular evidence for the presence of novel actinomycete lineages in a temperate forest soil. J Ind Microbiol 17:197–204
Mehling A, Wehmeier UF, Piepersberg W (1995) Nucleotide sequences of streptomycete 16S ribosomal DNA—towards a specific identification system for streptomycetes using PCR. Microbiology 141:2139–2147
Mexson, J, Goodfellow M, Bull AT (2000) Preliminary studies of the diversity of micromonosporae in Indonesian soils and lake sediments. Int J Biotechnol Special Issue, June, pp 384–388
Mincer TJ, Jensen PR, Kaufmann CA, Fenical W (2002) Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments. Appl Environ Microbiol 68:5005–5011
Monciardini P, Sosio M, Cavaletti L, Chiochini C, Donadio S (2002) New PCR primers for the selective amplification of 16S rDNA from different groups of actinomycetes. FEMS Microbiol Ecol 42:419–429
Montalvo NF, Mohamed NM, Enticknap JJ, Hill RT (2005) Novel actinobacteria from marine sponges. Antonie van Leeuwenhoek 87:29–36
Morón R, Gonzalez I, Genilloud O (1999) New genus-specific primers for the PCR identification of members of the genera Pseudonocardia and Saccharoplyspora. Int J Syst Bacteriol 49:149–162
Newman DJ (2008) Natural products as leads to potential drugs: an old process or the hope for drug discovery? J Med Chem 61:2589–2599
Newman DJ, Cragg GM (2007) Natural products as sources of new drugs over the last 25 years. J Nat Prod 70:461–477
Oh D-C, Gontang EA, Kaufman CA, Jensen PR, Fenical W (2008) Salinipyrones and pacificanones, mixed-precursor polypeptides from the marine actinomycete Salinispora pacifica. J Nat Prod 71:570–575
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
Olano C, Méndez C, Salas JA (2009a) Antitumor compounds from marine actinomycetes. Mar Drugs 7:210–248
Olano C, Mèndez C, Salas JA (2009b) Antitumor compounds from actinomycetes from gene clusters to new derivatives by combinatorial synthesis. Nat Prod Rep 26:628–660
Oliynyk M, Samborskyy M, Lester JB, Mironenko T, Scott N, Dickens S, Haydock SF, Leadley PJ (2007) Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL 23338. Nat Biotechnol 25:447–453
Ōmura S, Ikeda H, Ishikawa J et al (2001) Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Proc Natl Acad Sci 98:12215–12220
Pathom-aree W, Nogi Y, Sutcliffe IC, Ward AC, Horikoshi K, Bull AT, Goodfellow M (2006a) Williamsia marianensis sp. nov., a novel actinomycete isolated from the Mariana Trench. Int J Syst Evol Microbiol 56:1123–1126
Pathom-aree W, Nogi Y, Sutcliffe IC, Ward AC, Horikoshi K, Bull AT, Goodfellow M (2006b) Dermacoccus abyssi sp. nov., a piezotolerant actinomycette isolated from the Mariana Trench. Int J Syst Evol Microbiol 56:1233–1237
Pathom-aree W, Nogi Y, Ward AC, Horikoshi K, Bull AT, Goodfellow M (2006c) Dermacoccus barathri sp. nov. and Dermacoccus profundi sp. nov., novel actinomycetes isolated from deep-sea mud of the Mariana Trench. Int J Syst Evol Microbiol 56:2303–2307
Pathom-aree W, Stach JEM, Ward AC, Horikoshi K, Bull AT, Goodfellow M (2006d) Diversity of actinomycetes isolated from Challenger Deep sediment (10, 898 m) from the Mariana Trench. Extremophiles 10:181–189
Payne DJ, Bradley J, Edwards JE, Gilbert D, Scheld, Bartlett JG (2007) Drugs from bad bugs: confronting the challenges of antibacterial discovery. Nat Rev Drug Discov 6:29–40
Penn K, Jenkins C, Nett M, Udwary DW, Gontang EA et al (2009) Genomic islands link secondary metabolism to functional adaptation in marine actinomycetes. ISMEJ 3:1193–1203
Pimentel-Elardo SM, Scheuermayer M, Kozytska S, Hentschel U (2009) Streptomyces axinellse sp. nov., isolated from the Mediterranean sponge Axinella polyporides (Poriferae). Int J Syst Evol Microbiol 59:1433–1437
Priest FG (2004) Approaches to identification. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM Press, Washington, DC, pp 49–56
Priest FG, Goodfellow M (eds) (2000) Applied microbial systematics. Kluwer Academic Publishers, Dordrecht, pp 1–479
Qin S, Li J, Zhang Y-Q, Zhu W-Y, Zhao G-Z, Xu L-H, Li W-J (2009) Plantactinospora mayteni gen. nov., sp. nov., a member of the family Micromonosporaceae. Int J Syst Evol Microbiol 59:2527–2533
Qui D, Ruan J, Huang Y (2008) Selective isolation and identification of members of the genus Micromonospora. Appl Environ Microbiol 74:5593–5597
Riedlinger J, Reicke A, Zähner H, Krismer B, Bull AT, Maldonado LA, Ward AC, Goodfellow M, Bister B, Bischoff D, Süssmuth R, Fiedler H-P (2004) Abyssomicins, inhibitors of the para-aminobenzoic acid pathway produced by the marine Verrucosispora strain AB-18-032. J Antibiot 57:271–279
Rowbotham TJ, Cross T (1977) Ecology of Rhodococcus coprophilus and associated actinomycetes in freshwater and agricultural habitats. J Gen Microbiol 100:231–240
Salanoubat M, Genin F, Arliguenave F, Gouzy J, Mangenot S et al (2002) Genome sequence of the plant pathogen Ralstonia solanacearum. Nature 415:497–502
Salazar O, Morón R, Genilloud O (2000) New genus-specific primers for the PCR identification of members of the genus Saccharomonospora and evaluation of the diversity of wild-type isolates of Saccharomonospora detected from soil DNAs. Int J Syst Evol Microbiol 50:2043–2053
Salt M, Hugenholz P, Janssen PH (2002) Cultivation of globally distributed soil bacteria phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol 4:654–656
Schleifer K-H (2010) Classification of Bacteria and Archaea: past, present and future. Syst Appl Microbiol 32:533–542
Schloss PD, Handelsman J (2005) Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol 6:229–232
Schneider K, Keller S, Wolter FE, Röglin L, Beil W, Seitz O, Nicholson G, Bruntner C, Riedlinger J, Fiedler H-P, Süssmuth RD (2008) Proximicins A, B and C—antitumor furan analogues of netropsin from the marine actinomycete Verrucosispora induce upregulation of p53 and the cyclin kinase inhibitor p21. Angew Chem Int Ed 47:3258–3261
Schneider K, Nachtigall J, Hänchen A, Nicholson G, Goodfellow M, Süssmuth RD, Fiedler H-P (2009) Lipocarbazoles, new secondary metabolites from Tsukamurella pseudospumae Acta 1857 with antioxidative activity. J Nat Prod 72:1768–1772
Sembiring L, Ward AC, Goodfellow M (2000) Selective isolation and characterisation of members of the Streptomyces violaceusniger clade associated with the roots of Paraserianthes falcataria. Antonie van Leeuwenhoek 78:353–366
Seo YB, Kim D-E, Kim G-D, Kim H-W, Nam S-W, Kim YT, Lee HJ (2009) Kocuria givangalliensis sp. nov., an actinobacterium isolated from seawater. Int J Syst Evol Microbiol 59:2769–2772
Seviour RJ, Kragelund C, Long Y, Eales K, Nielsen JL, Nielsen PH (2008) Ecophysiology of actinobacteria in activated sludge systems. Antonie van Leeuwenhoek 94:21–33
Shen FT, Young C-C (2005) Rapid detection and identification of the metabolically diverse genus Gordonia by 16S rRNA-gene-targeted genus-specific primers. FEMS Microbiol Lett 250:221–227
Skerman VBD, McGowan V, Sneath PHA (1980) Approved lists of bacterial names. Int J Syst Bacteriol 30:225–420
Sneath PHA (2005) Bacterial nomenclature. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology, 2nd edn, vol 2, part A, introductory essays. Springer, USA, pp 83–88
Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the unexplored “rare biosphere”. Proc Natl Acad Sci USA 103:12115–12120
Stach JEM, Bull AT (2005) Estimating and comparing the diversity of marine actinobacteria. Antonie van Leeuwenhoek 87:3–9
Stach JEM, Maldonado LA, Ward AC, Goodfellow M, Bull AT (2003a) New primers specific for Actinobacteria: application to marine and terrestrial environments. Environ Microbiol 5:828–841
Stach JEM, Maldonado LA, Masson DG, Ward AC, Goodfellow M, Bull AT (2003b) Statistical approaches for estimating actinobacterial diversity in marine sediments. Appl Environ Microbiol 69:6189–6200
Stach JEM, Maldonado LA, Ward AC, Bull AT, Goodfellow M (2004) Williamsia maris sp. nov., a novel actinomycete isolated from the Sea of Japan. Int J Syst Evol Microbiol 54:191–194
Stackebrandt E, Schumann P (2006) Introduction to the taxonomy of Actinobacteria. In: Dworkin M, Falkow S, Schleifer RH, Stackebrandt RM (eds) The prokaryotes, 3rd edn, vol 3, Archaea and Bacteria: Firmicutes, Actinomycetes. Springer, New York, pp 297–321
Staley JT (2006) The bacterial species dilemma and the genomic-phylogenetic species concept. Philos Trans R Soc B 361:1899–1909
Stingl U, Cho J-C, Foo W, Vergin KL, Lanoil B, Giovannoni SJ (2008) Dilution-to-extinction of psychrotolerant planktonic bacteria from permanently ice-covered lakes in the McMurdo Dry Valleys, Antarctica. Microb Ecol 55:395–405
Stover CK, Pham XQ, Erwin AL, Mizoguishi SD, Warrener P et al (2000) Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406:959–964
Strohl WR (2004) Antimicrobials. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM Press, Washington, DC, pp 336–355
Suzuki S-I, Okuda T, Komatsubara S (2001a) Selective isolation and distribution of the genus Planomonospora in soils. Can J Microbiol 47:253–263
Suzuki S-I, Okuda T, Komatsubara S (2001b) Selective isolation and study of the global distribution of the genus Planobispora in soils. Can J Microbiol 47:979–986
Talbot GH, Bradley J, Edwards JE Jr, Gilbert D, Scheld M, Bartlett JG (2006) Bad bugs need drugs: an update of the development pipeline from the antimicrobial task force of the Infectious Diseases Society of America. Clin Infect Dis 42:657–668
Tamura T, Ishida Y, Norzawa Y, Otoguro M, Suzuki K-I (2009) Transfer of Actinomadura spadix Nonomura and Ohara 1971 to Actinoallomurus spadix gen. nov., comb. nov., and description of Actinoallomurus amamiensis sp. nov., Actinoallomurus caesius sp. nov., Actinoallomurus coprocola sp. nov., Actinoallomurus fulvus sp. nov., Actinoallomurus iriomotensis sp. nov., Actinoallomurus luridus sp. nov., Actinoallomurus purpureus sp. nov. and Actinoallomurus yoronensis sp. nov. Int J Syst Evol Microbiol 59:1867–1874
Tan GYA, Robinson S, Lacey E, Goodfellow M (2006) Exploration of Amycolatopsis diversity in soil using genus-specific primers and novel selective media. Syst Appl Microbiol 29:557–569
Tan GYA, Robinson S, Lacey E, Brown W, Kim W, Goodfellow M (2007) Amycolatopsis regifaucium sp. nov., a novel actinomycete that produces kigamicins. Int J Syst Evol Microbiol 57:2562–2567
The Society for Actinomycetes Japan (2001) Identification manual of actinomycetes. Business Center for Academic Societies, Tokyo
Theobald U, Schimana J, Fiedler H-P (2000) Microbial growth and production kinetics of Streptomyces antibioticus Tu 6040. Antonie van Leeuwenhoek 78:307–313
Tian X-P, Tang S-K, Dong J-D, Zhang Y-Q, Xu L-H, Zhang S, Li W-J (2009a) Marinactinospora thermotolerans gen. nov., sp. nov., a marine actinomycete isolated from a sediment in the northern South China Sea. Int J Syst Evol Microbiol 59:948–952
Tian X-P, Zhi X-Y, Qiu Y-Q, Zhang Y-Q, Tang S-K, Xu L-H, Zhang S, Li W-J (2009b) Sciscionella marina gen. nov., sp. nov., a marine actinomycete isolated from a sediment in the northern South China Sea. Int J Syst Evol Microbiol 59:222–228
Tindall BJ, Roseselló-Mora R, Busse HJ, Ludwig W, Kämpfer P (2010) Notes on the characterization of prokaryotic strains for taxonomic purposes. Int J Syst Evol Microbiol 80:249–266
Trüper H (1999) How to name a prokaryote? Etymological considerations, proposals and practical advice in prokaryotic nomenclature. FEMS Microbiol Rev 23:231–249
Trüper H (2005) Etymology in nomenclature of prokaryotes. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology, 2nd edn, vol 2, the proteobacteria, part A, introductory essays. Springer, USA, pp 89–99
Udwary DW, Ziegler L, Asolbar HN, Singan V, Lapidus A, Fenical W, Jensen PR, Moore BS (2007) Genome sequencing reveals complete secondary metabolome in the marine actinomycete Salinispora tropica. Proc Natl Acad Sci USA 104:10376–10381
Ue H, Matsuo Y, Kasai H, Yokota A (2010) Miniimonas arenae gen. nov., sp. nov., a novel actinobacterium isolated from sea sand. Int J Syst Evol Microbiol. doi: 10.1099/ijs.0.019596-0
Vandamme P, Pot P, Gillis M, de Vos P, Kersters K, Swings J (1996) Polyphasic taxonomy: a consensus approach to bacterial systematics. Microbiol Rev 60:407–438
Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, van Sinderen D (2007) Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev 71:495–548
Vickers JC, Williams ST (1987) An assessment of plate inoculation procedures for the enumeration and selective isolation of streptomycetes. Microbios Lett 35:113–117
Vickers JC, Williams ST, Ross GW (1984) A taxonomic approach to selective isolation of streptomycetes from soil. In: Ortiz-Ortiz L, Bojalil LF, Yakoleff V (eds) Biological, biochemical and biomedical of actinomycetes. Academic Press, London, pp 553–561
Ward AC, Goodfellow M (2004) Phylogeny and functionality: taxonomy as a roadmap to genes. In: Bull AT (ed) Microbial diversity, bioprospecting. ASM Press, Washington, DC, pp 288–313
Watve MG, Tickoo R, Jog MM, Bhole BD (2001) How many antibiotics are produced by the genus Streptomyces. Arch Microbiol 176:386–390
Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464
Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583
Williams PG (2008) Panning for chemical gold: marine bacteria as a source of new therapeutics. Trends Biotechnol 27:45–51
Williams ST, Vickers JC (1988) Detection of actinomycetes in the natural environment: problems and perspectives. In: Okami Y, Beppu T, Ogawara K (eds) Biology of actinomycetes. Japan Scientific Societies Press, Tokyo, pp 265–270
Williams ST, Davies FL, Hall DM (1969) A practical approach to the taxonomy of actinomycetes isolated from soil. In: Sheals JG (ed) The soil ecosystem. The Systematics Association, London, pp 107–117
Williams PG, Asolkar RN, Kondratyuk T, Pezzulo JM, Jensen PR, Fenical W (2007) Saliniketals A and B, bicyclic polyketides from the marine actinomycete Salinispora arenicola. J Nat Prod 70:83–88
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E et al (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nat Lett 426:1056–1060
Xu J, Wang Y, Xie S-J, Xu J, Xiao J, Ruan J-S (2009) Streptomyces xiamenensis sp. nov., isolated from a mangrove sediment. Int J Syst Evol Microbiol 59:472–476
Yi H, Schumann P, Sohn K, Chun J (2004) Serinicoccus marinus gen. nov., sp. nov., a novel actinomycete with L-ornithine and L-serine in the peptidoglycan. Int J Syst Evol Microbiol 54:1585–1589
Yi H, Schumann P, Chun J et al (2007) Demequina aestuarii gen. nov., sp. nov., a novel actinomycete of the suborder Micrococcineae, and reclassification of Cellulomonas fermentaris Bagnara et al. 1985 as Actinotalea fermentaris gen. nov., comb. nov. Int J Syst Evol Microbiol 57:151–156
Yoon JH, Lee ST, Shin YK, Kim SB, Kim HJ, Goodfellow M, Park YH (1996) Rapid identification of Saccharomonospora strains by multiplex PCR using species-specific primers within the 16S rRNA gene. J Microbiol Methods 27:89–95
Zhang H, Lee YK, Zhang W, Lee HK (2006) Culturable actinobacteria from the marine sponge Hymeniacidon perleve: isolation and phylogenetic diversity by 16S rRNA gene-RFLP analysis. Antonie van Leeuwenhoek 90:159–169
Zhi X-Y, Li W-J, Stackebrandt E (2009) An update on the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 59:589–608