Phylogenetic diversity and biological activity of actinobacteria isolated from the chukchi shelf marine sediments in the arctic ocean

Marine Drugs

Volumn 12, Issue 3, 2014, Pages 1281-1297

  Yuan, Meng ^a,b   Yu, Yong ^a   Li, Hui Rong ^a   Dong, Ning ^a,b   Zhang, Xiao Hua ^b  

^a POLAR RESEARCH INSTITUTE OF CHINA   (China)

^b OCEAN UNIVERSITY OF CHINA   (China)

Author keywords

Arctic ocean; Biological activity; Marine actinobacteria; Phylogenetic diversity

Indexed keywords

RNA 16S;

16S RRNA GENE; ACTINOBACTERIA; AGROCOCCUS; ANTIBACTERIAL ACTIVITY; ANTIFUNGAL ACTIVITY; ANTIMICROBIAL ACTIVITY; ARCTIC OCEAN; ARSENICICOCCUS; ARTHROBACTER; ARTICLE; BACILLUS SUBTILIS; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM ISOLATION; BREVIBACTERIUM; CANDIDA ALBICANS; CHUKCHI SHELF MARINE SEDIMENT; CITRICOCCUS; DNA FINGERPRINTING; GENE SEQUENCE; GENETIC MANIPULATION; GENETIC VARIABILITY; JANIBACTER; KOCURIA; MICROBACTERIUM; MICROBIAL DIVERSITY; MICROLUNATUS; NOCARDIOIDES; NOCARDIOPSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OCEANIC REGIONS; PHYLOGENY; SACCHAROPOLYSPORA; SALINIBACTERIUM; SEDIMENT; STREPTOMYCES;

ACTINOBACTERIA; ANTI-INFECTIVE AGENTS; ARCTIC REGIONS; BIODIVERSITY; CENTRIFUGATION; CULTURE MEDIA; DNA PRIMERS; ECOSYSTEM; GEOLOGIC SEDIMENTS; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEAWATER;

EID: 84897071855     PISSN: None     EISSN: 16603397     Source Type: Journal    
DOI: 10.3390/md12031281     Document Type: Article

References (51)

1. Ventura, M.; Canchaya, C.; Tauch, A.; Chandra, G.; Fitzgerald, G.F.; Chater, K.F.; van Sinderen, D. Genomics of Actinobacteria: Tracing the evolutionary history of an ancient phylum. Microbiol. Mol. Biol. Rev. 2007, 71, 495-548.
2. Bérdy, J. Bioactive microbial metabolites. J. Antibiot. 2005, 58, 1-26.
3. Fiedler, H.-P.; Bruntner, C.; Bull, A.T.; Ward, A.C.; Goodfellow, M.; Potterat, O.; Puder, C.; Mihm, G. Marine actinomycetes as a source of novel secondary metabolites. Antonie van Leeuwenhoek 2005, 87, 37-42. (Pubitemid 40331510)
4. Lam, K.S. Discovery of novel metabolites from marine actinomycetes. Curr. Opin. Microbiol. 2006, 9, 245-251. (Pubitemid 43817620)
5. Bull, A.T.; Stach, J.E.M. Marine actinobacteria: New opportunities for natural product search and discovery. Trends Microbiol. 2007, 15, 491-499. (Pubitemid 350102189)
6. Stach, J.E.M.; Bull, A.T. Estimating and comparing the diversity of marine actinobacteria. Antonie van Leeuwenhoek 2005, 87, 3-9. (Pubitemid 40331506)
7. Goodfellow, M.; Fiedler, H.-P. A guide to successful bioprospecting: Informed by actinobacterial systematics. Antonie van Leeuwenhoek 2010, 98, 119-142.
8. Fenical1, W.; Jensen, P.R. Developing a new resource for drug discovery: Marine actinomycete bacteria. Nat. Chem. Biol. 2006, 2, 666-673.
9. Olano, C.; Méndez, C.; Salas, J.A. Antitumor compounds from marine actinomycetes. Mar. Drugs 2009, 7, 210-248.
10. Fattorusso, E.; Taglialatela-Scafati, O. Marine antimalarials. Mar. Drugs 2009, 7, 130-152.
11. Rahman, H.; Austin, B.; Mitchell, W.J.; Morris, P.C.; Jamieson, D.J.; Adams, D.R.; Spragg, A.M.; Schweizer, M. Novel anti-infective compounds from marine bacteria. Mar. Drugs 2010, 8, 498-518.
12. Xiong, Z.-Q.; Wang, J.-F.; Hao, Y.-Y.; Wang, Y. Recent advances in the discovery and development of marine microbial natural products. Mar. Drugs 2013, 11, 700-717.
13. Weyland, H. Distribution of Actinomycetes on the Sea Floor. In Actinomycetes: Proceedings of the Fourth International Symposium on Actinomycete Biology, Cologne, September 3-7, 1979; Schaal, K.P., Pulverer, G., Eds.; Gustav Fischer Verlag: Stuttgart, Germany, 1981; pp. 185-193.
14. Yu, Y.; Li, H.; Zeng, Y.; Chen, B. Isolation and phylogenetic assignation of actinomycetes in the marine sediments from the Arctic Ocean. Acta Oceanol. Sin. 2005, 24, 135-142. (Pubitemid 43072404)
15. Bredholdt, H.; Galatenko, O.A.; Engelhardt, K.; Tjaervik, E.; Terekhova, L.P.; Zotchev, S.B. Rare actinomycete bacteria from the shallow water sediments of the Trondheim fjord, Norway: Isolation, diversity and biological activity. Environ. Microbiol. 2007, 9, 2756-2764. (Pubitemid 47547543)
16. Bredholdt, H.; Tjaervik, E.; Johnsen, G.; Zotchev, S.B. Actinomycetes from sediments in the Trondheim fjord, Norway: Diversity and biological activity. Mar. Drugs 2008, 6, 12-24. (Pubitemid 351543687)
17. Jørgensen, H.; Fjærvik, E.; Hakvåg, S.; Bruheim, P.; Bredholt, H.; Klinkenberg, G.; Ellingsen, T.E.; Zotchev, S.B. Candicidin biosynthesis gene cluster is widely distributed among Streptomyces spp. isolated from the sediments and the neuston layer of the Trondheim fjord, Norway. Appl. Environ. Microbiol. 2009, 75, 3296-3303.
18. Jørgensen, H.; Degnes, K.F.; Dikiy, A.; Fjærvik, E.; Klinkenberg, G.; Zotchev, S.B. Insights into the evolution of macrolactam biosynthesis through cloning and comparative analysis of the biosynthetic gene cluster for a novel macrocyclic lactam, ML-449. Appl. Environ. Microbiol. 2010, 76, 283-293.
19. Engelhardt, K.; Degnes, K.F.; Kemmler, M.; Bredholt, H.; Fjærvik, E.; Klinkenberg, G.; Sletta, H.; Ellingsen, T.E.; Zotchev, S.B. Production of a new thiopeptide antibiotic, TP-1161, by a marine Nocardiopsis sspecies. Appl. Environ. Microbiol. 2010, 76, 4969-4976.
20. Hakvåg, S.; Fjærvik, E.; Josefsen, K.D.; Ian, E.; Ellingsen, T.E.; Zotchev, S.B. Characterization of Streptomyces spp. isolated from the sea surface microlayer in the Trondheim fjord, Norway. Mar. Drugs 2008, 6, 620-635. (Pubitemid 352774418)
21. Wayne, L.G.; Brenner, D.J.; Colwell, R.R.; Grimont, P.A.D.; Kandler, O.; Krichevsky, M.I.; Moore, L.H.; Moore, W.E.C.; Murray, R.G.E.; Stackebrandt, E.; et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Evol. Microbiol. 1987, 37, 463-464.
22. Stackebrandt, E.; Goebel, B.M. Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 1994, 44, 846-849. (Pubitemid 24315169)
23. Stackebrandt, E.; Ebers, J. Taxonomic parameters revisited: Tarnished gold standards. Microbiol. Today 2006, 33, 152-155.
24. Wang, Y.X.; Cai, M.; Zhi, X.Y.; Zhang, Y.Q.; Tang, S.K.; Xu, L.H.; Cui, X.L.; Li, W.J. Microlunatus aurantiacus sp. nov., a novel actinobacterium isolated from a rhizosphere soil sample. Int. J. Syst. Evol. Microbiol. 2008, 58, 1873-1877.
25. Chen, L.; Li, S.U.; Xue, Y.F. Characterization of an alkaliphilic biosurfactant- producing strain of Dietzia. Microbiol. China 2012, 39, 1573-1579.
26. Ratnakar, N.A.; Dirk, S.; Rolf, H.; Siegmund, L.; Irene, W.D.; Hartmut, L. Helquinoline, a new tetrahydroquinoline antibiotic from Janibacter limosus Hel 1+. J. Antibiot. 2004, 57, 17-23.
27. Rojas, J.L; Martín, J.; Tormo, J.R.; Vicente, F, Brunati, M.; Ciciliato, I.; Losi, D.; Van, T.S.; Mergaert, J.; Swings, J.; et al. Bacterial diversity from benthic mats of Antarctic lakes as a source of new bioactive metabolites. Mar. Genomics 2009, 2, 33-41.
28. Fu, P.; Liu, P.; Gong, Q.H.; Wang, Y.; Wang, P.; Zhu, W.M. α-Pyrones from the marine-derived actinomycete Nocardiopsis dassonvillei subsp. dassonvillei XG-8-1. RSC Adv. 2013, 3, 20726-20731.
29. Augustine, S.K.; Bhavsar, S.P.; Kapadnis, B.P. A non-polyene antifungal antibiotic from Streptomyces albidoflavus PU 23. J. Biosci. 2005, 30, 201-211. (Pubitemid 40592638)
30. Yan, L.L.; Han, N.N.; Zhang, Y.Q.; Yu, L.Y.; Chen, J.; Wei, Y.Z.; Li, Q.P.; Tao, L.; Zheng, G.H.; Yang, S.E.; et al. Antimycin A18 produced by an endophytic Streptomyces albidoflavus isolated from a mangrove plant. J. Antibiot. 2010, 63, 259-261.
31. Yuan, M.; Dong, N.; Li, H.R.; Yu, Y. Sequence-based analysis of secondary-metabolite biosynthesis in actinobacteria isolated from Chukchi shelf marine sediments. Adv. Polar Sci. 2014, submitted for publication.
32. Hornung, A.; Bertazzo, M.; Dziarnowski, A.; Schneider, K.; Welzel, K.; Wohlert, S.E.; Holzenkämpfer, M.; Nicholson, G.J.; Bechthold, A.; Süssmuth, R.D.; et al. A Genomic screening approach to the structure-guided identification of drug candidates from natural sources. Chembiochem 2007, 8, 757-766. (Pubitemid 47183632)
33. Stockmann, M.; Piepersberg, W. Gene probes for the detection of 6-deoxyhexose metabolism in secondary metabolite-producing streptomycetes. FEMS Microbiol. Lett. 1992, 90, 185-189.
34. Lee, M.Y.; Myeong, J.S.; Park, H.J.; Han, K.; Kim, E.S. Isolation and partial characterization of a cryptic polyene gene cluster in Pseudonocardia autotrophica. J. Ind. Microbiol. Biotechnol. 2006, 33, 84-87.
35. Dairi, T.; Hamano, Y.; Igarashi, Y.; Furumai, T.; Oki, T. Cloning and nucleotide sequence of the putative polyketide synthase genes for pradimicin biosynthesis from Actinomadura hibisca. Biosci. Biotechnol. Biochem. 1997, 61, 1445-1453. (Pubitemid 127472960)
36. Kallifidas, D.; Kang, H.S.; Brady, S.F. Tetarimycin A, an MRSA-Active antibiotic identified through induced expression of environmental DNA gene clusters. J. Am. Chem. Soc. 2012, 134, 19552-19555.
37. Clardy, J.M.; Fischbach, A.; Walsh, C.T. New antibiotics from bacterial natural products. Nat. Biotechnol. 2006, 24, 1541-1550. (Pubitemid 44967478)
38. Hopkins, D.W.; McNaughton, S.J.; O'Donnell, A.G. A dispersion and differential centrifugation technique for representatively sampling microorganisms from soil. Soil Biol. Biochem. 1991, 23, 217-225.
39. Versalovic, J.; Schneider, M.; de Bruijn, F.J.; Lupski, J.R. Genomic fingerprinting of bacteria using repetitive sequencebased polymerase chain reaction. Methods Mol. Cell. Biol. 1994, 5, 24-40.
40. Rademaker, J.L.W.; Hoste, B.; Louws, F.J.; Kersters, K.; Swings, J.; Vauterin, L.; Vauterin, P.; de Bruijn, F.J. Comparison of AFLP and rep-PCR genomic fingerprinting with DNA-DNA homology studies: Xanthomonas as a model system. Int. J. Syst. Evol. Microbiol. 2000, 50, 665-677.
41. Lane, D.J. 16S/23S rRNA Sequencing. In Nucleic Acid Techniques in Bacterial Systematics; Stackebrandt, E., Goodfellow, M., Eds.; Wiley: Chichester, UK, 1991; pp. 115-175.
42. Kim, O.S.; Cho, Y.J.; Lee, K.; Yoon, S.H.; Kim, M.; Na, H.; Park, S.C.; Jeon, Y.S.; Lee, J.H.; Yi, H.; et al. Introducing EzTaxon-e: A prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbiol. 2012, 62, 716-721.
43. EzTaxon Server version 2.1. Available online: http://eztaxon-e ezbiocloud.net (accessed on 1 November 2013).
44. NCBI database. Available online: http://www.ncbi.nlm.nlh.gov (accessed on 1 November 2013).
45. Tamura, K.; Peterson, D.; Peterson, N.; Stecher, G.; Nei, M.; Kumar, S. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 10, 2731-2739.
46. Schneemann, I.; Nagel, K.; Kajahn, I.; Labes, A.; Wiese, J.; Imhoff, J.F. Comprehensive investigation of marine actinobacteria associated with the sponge Halichondria panacea. Appl. Environ. Microbiol. 2010, 76, 3702-3714.
47. Izumikawa, M.; Murata, M.; Tachibana, K.; Ebizuka, Y.; Fujii, I. Cloning of modular type I polyketide synthase genes from salinomycin producing strain of Streptomyces albus. Bioorg. Med. Chem. 2003, 11, 3401-3405. (Pubitemid 36870980)
48. Wawrik, B.; Kerkhof, L.; Zylstra, G.J.; Kukor, J.J. Identification of unique type II polyketide synthase genes in soil. Appl. Environ. Microbiol. 2005, 71, 2232-2238. (Pubitemid 40646960)
49. Ayuso-Sacido, A.; Genilloud, O. New PCR primers for the screening of NRPS and PKS-I systems in actinomycetes: Detection and distribution of these biosynthetic gene sequences in major taxonomic groups. Microb. Ecol. 2005, 49, 10-24. (Pubitemid 40747800)
50. Schneemann, I.; Wiese, J.; Kunz, A.L.; Imhoff, J.F. Genetic approach for the fast discovery of phenazine producing bacteria. Mar. Drugs 2011, 9, 772-789.
51. Du, Y.; Li, T.; Wang, Y.G.; Xia, H. Identification and functional analysis of dTDP-glucose-4, 6-dehydratase gene and its linked gene cluster in an aminoglycoside antibiotics producer of Streptomyces tenebrarius H6. Curr. Microbiol. 2004, 49, 99-107. (Pubitemid 38970714)