Culturability and Secondary Metabolite Diversity of Extreme Microbes: Expanding Contribution of Deep Sea and Deep-Sea Vent Microbes to Natural Product Discovery

Marine Biotechnology

Volumn 13, Issue 1, 2011, Pages 1-11

  Pettit, Robin K ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

Author keywords

Deep sea hydrothermal vent; Extremophile; Natural product; Secondary metabolite

Indexed keywords

ARCHAEA; CHROMAN DERIVATIVES; CULTURABILITY; CULTURE CONDITIONS; DEEP SEA; DEEP-SEA HYDROTHERMAL VENTS; EXTREME ENVIRONMENT; EXTREMOPHILES; HIGH TEMPERATURE; HIGH-PRESSURE ENVIRONMENT; NATURAL PRODUCTS; PHYLOGENETIC DIVERSITY; SECONDARY METABOLITE; SECONDARY METABOLITES; SIDEROPHORES;

BACTERIOLOGY; BIOMOLECULES; ECOLOGY; HOT SPRINGS; METABOLISM; METABOLITES; VENTS;

BACTERIA;

BIOLOGICAL PRODUCT; SEA WATER;

BIOACTIVITY; BIOTECHNOLOGY; DEEP SEA; EXTREMOPHILE; HIGH PRESSURE; HIGH TEMPERATURE; HYDROTHERMAL VENT; MARINE TECHNOLOGY; MICROBIAL COMMUNITY; PHYLOGENETICS; SECONDARY METABOLITE; SIDEROPHORE;

ADAPTATION; ARCHAEON; BACTERIUM; CHEMISTRY; CLASSIFICATION; ECOSYSTEM; FUNGUS; GEOGRAPHIC AND GEOLOGICAL PHENOMENA; HEAT; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; REVIEW;

ADAPTATION, PHYSIOLOGICAL; ARCHAEA; BACTERIA; BIOLOGICAL AGENTS; ECOSYSTEM; FUNGI; GEOLOGICAL PHENOMENA; HOT TEMPERATURE; SEAWATER;

ARCHAEA; BACTERIA (MICROORGANISMS); FUNGI;

EID: 79952283235     PISSN: 14362228     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10126-010-9294-y     Document Type: Review

References (81)

1. Abken H-J, Tietze M, Brodersen J, Bäumer S, Beifuss U, Deppenmeier U (1998) Isolation and characterization of methanophenazine and function of phenazines in membrane-bound electron transport of Methanosarcina mazei Gö1. J Bact 180: 2027-2032.
2. Andrianasolo EH, Haramaty L, Rosario-Passapera R, Bidle K, White E, Vetriani C, Falkowski P, Lutz R (2009) Ammonificins A and B, hydroxyethylamine chroman derivatives from a cultured marine hydrothermal vent bacterium, Thermovibrio ammonificans. J Nat Prod 72: 1216-1219.
3. Aragozzini F, Manachini PL, Craveri R, Rindone B, Sclastico C (1972) Structure of thermozymocidin. Experientia 28: 881-882.
4. Atomi H (2005) Recent progress towards the application of hyperthermophiles and their enzymes. Curr Opin Chem Biol 9: 166-173.
5. Beifuss U, Tietze M (2005) Methanophenazine and other natural biologically active phenazines. Top Curr Chem 244: 77-113.
6. Burgaud G, Calvez TL, Arzur D, Vandenkoornhuyse P, Barbier G (2009) Diversity of culturable marine filamentous fungi from deep-sea hydrothermal vents. Environ Microbiol 11: 1588-1600.
7. Campbell BJ, Jeanthon C, Kostka JE, Luther GW III, Cary SC (2001) Growth and phylogenetic properties of novel bacteria belonging to the epsilon subdivision of the Proteobacteria enriched from Alvinella pompejana and deep-sea hydrothermal vents. Appl Environ Microbiol 67: 4566-4572.
8. Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, Cary SC (2009) Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genet 5: e1000362.
9. Comita PB, Gagosian RB, Pang H, Costello CE (1984) Structural elucidation of a unique macrocyclic membrane lipid from a new, extremely thermophilic, deep-sea hydrothermal vent archaebacterium, Methanococcus jannaschii. J Biol Chem 24: 15234-15241.
10. Cornec L, Loaec M, Rougeaux H, Guezennec J, Dietrich J (1997) Molecules from hydrothermal micro-organisms of potential to biotechnology: polysaccharides and heat-stable enzymes. Océanis 23: 11-25.
11. Cornec L, Robineau J, Rolland JL, Dietrich J, Barbier G (1998) Thermostable esterases screened on hyperthermophilic archaeal and bacterial strains isolated from deep-sea hydrothermal vents: characterization of esterase activity of a hyperthermophilic archaeum Pyrococcus abyssi. J Mar Biotech 6: 104-110.
12. Cragg GM, Newman DJ (2009) Nature: a vital source of leads for anticancer drug development. Phytochem Rev 8: 313-331.
13. Cragg GM, Grothaus PG, Newman DJ (2009) Impact of natural products on developing new anti-cancer agents. Chem Rev 109: 3012-3043.
14. Crapart S, Fardeau ML, Cayol JL, Thomas P, Sery C, Ollivier B, Combet-Blanc Y (2007) Exiguobacterium profundum sp. nov., a moderately thermophilic, lactic acid-producing bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 57: 287-292.
15. Craveri R, Manachini PL, Aragozzini F (1972) Thermozymocidin new antifungal antibiotic from a thermophilic eumycete. Experientia 28: 867-868.
16. Crespo-Medina M, Chatziefthimiou A, Cruz-Matos R, Pérez-Rodríguez I, Barkay T, Lutz R, Starovoytov V, Vetriani C (2009) Salinisphaera hydrothermalis sp. nov., a mesophilic, halotolerant, facultatively autotrophic, thiosulfate-oxidixing gammaproteobacterium from deep-sea hydrothermal vents, and emended description of the genus Salinisphaera. Intl J Syst Evol Microbiol 59: 1497-1503.
17. Cui CB, Kakeya H, Okada G, Onose R, Osada H (1996) Novel mammalian cell cycle inhibitors, tryprostatins A, B and other diketopiperazines produced by Aspergillus fumigatus. I. Taxonomy, fermentation, isolation and biological properties. J Antibiot 49: 527-533.
18. Davidson BS, Schumacher RW (1993) Isolation and synthesis of caprolactins A and B, new caprolactams from a marine bacterium. Tetrahed 49: 6569-6574.
19. Du L, Li D, Zhu T, Cai S, Wang F, Xiao X, Gu Q (2009) New alkaloids and diterpenes from a deep ocean sediment derived fungus Penicillium sp. Tetrahed 65: 1033-1039.
20. Durand P, Reysenbach AL, Prieur D, Pace N (1993) Isolation and characterization of Thiobacillus hydrothermalis sp. nov., a mesophilic obligately chemolithotrophic bacterium isolated from a deep-sea hydrothermal vent in Fiji Basin. Arch Microbiol 159: 39-44.
21. Edgcomb VP, Kysela DT, Teske A, de Vera GA, Sogin ML (2002) Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. PNAS 99: 7658-7662.
22. Eprintsev AT, Falaveeva MI, Parfyonova NV (2005) Malate dehydrogenase from the thermophilic bacterium Vulcanithermus medioatlanticus. Biochem (Moscow) 70: 1027-1030.
23. Gadanho M, Sampaio JP (2005) Occurrence and diversity of yeasts in the mid-Atlantic ridge hydrothermal fields near the Azores archipelago. Microb Ecol 50: 408-417.
24. Gantelet H, Ladrat C, Godfroy A, Barbier G, Duchiron F (1998) Characteristics of pullulanases from extremely thermophilic archaea isolated from deep-sea hydrothermal vents. Biotech Lett 20: 819-823.
25. Gärtner A, Wiese J, Imhoff JF (2008) Amphritea atlantica gen. nov., sp. nov., a gammaproteobacterium from the Logatchev hydrothermal vent field. Int J Syst Evol Microbiol 58: 34-39.
26. Gautschi JT, Amagata T, Amagata A, Valeriote FA, Mooberry SL, Crews P (2004) Expanding the strategies in natural product studies of marine-derived fungi: a chemical investigation of Penicillium obtained from deep water sediment. J Nat Prod 67: 362-367.
27. Gonthier I, Rager M-N, Metzger P, Guezennec J, Largeau C (2001) A di-O-dihydrogeranylgeranyl glycerol from Thermococcus S 557, a novel ether lipid, and likely intermediate in the biosynthesis of diethers in Archaea. Tetrahed 42: 2795-2797.
28. Grzymski JJ, Murray AE, Campbell BJ, Kaplarevic M, Gao GR, Lee C, Daniel R, Ghadiri A, Feldman RA, Cary SC (2008) Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility. PNAS 105: 17516-17521.
29. Guezennec J (2002) Deep-sea hydrothermal vents: a new source of innovative bacterial exopolysaccharides of biotechnological interest? J Ind Microbiol Biotech 29: 204-208.
30. Hafenbradl D, Keller M, Stetter KO, Hammann P, Hoyer F, Kogler H (1996) Sibyllimycine, 5, 6, 7, 8-Tetrahydro-3-methyl-8-0x0-4-azaindolizidine, a novel metabolite from Thermoactinomyces sp. Angew Chem Int 35: 545-547.
31. Hohmann C, Schneider K, Brunter 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 (2009) Caboxamycin, a new antibiotic of the benzoxazole family produced by the deep-sea strain Streptomyces sp. NTK 937. J Antibiot 62: 99-104.
32. Homann VV, Sandy M, Tincu JA, Templeton AS, Tebo BM, Butler A (2009) Loihichelins A-F, a suite of amphiphilic siderophores produced by the marine bacterium Halomonas LOB-5. J Nat Prod 72: 884-888.
33. Jannasch HW, Wirsen CO, Nelson DC, Robertson LA (1985) Thiomicrospira crunogena sp. nov., a colorless, sulfur-oxidizing bacterium from a deep-sea hydrothermal vent. Int J Syst Bacteriol 35: 422-424.
34. Jeong SY, Shin HJ, Kim TS, Lee HS, Park SK, Kim HM (2006) Streptokordin, a new cytotoxic compound of the methylpyridine class from a marine-derived Streptomyces sp. KORDI-3238. J Antibiot 59: 234-240.
35. Kicklighter CE, Fisher CR, Hay ME (2004) Chemical defense of hydrothermal vent and hydrocarbon seep organisms: a preliminary assessment using shallow-water consumers. Mar Ecol Prog Ser 275: 11-19.
36. Kohama Y, Teramoto T, Iida K, Muayama N, Semba T, Tatebatake N, Kayamori Y, Tsujikawa K, Mimura T (1991) Isolation of a new antitumor substance from Bacillus stearothermophilus. Chem Pharm Bull 39: 2468-2470.
37. Kohama Y, Iida K, Tanaka K, Semba T, Itoh M, Teramoto T, Tsujikawa K, Mimura T (1993) Studies on thermophile products. VI. Activation of mouse peritoneal macrophages by bis(2-hydroxyethyl) trisulfide. Biol Pharm Bull 16: 973-977.
38. Kuwabara T, Minaba M, Ogi N, Kamekura M (2007) Thermococcus celericrescens sp. nov., a fast-growing and cell-fusing hyperthermophilic archaeon from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 57: 437-443.
39. Li D, Cai S, Tian L, Lin Z, Zhu T, Fang Y, Liu P, Gu Q, Zhu W (2007a) Two new metabolites with cytotoxicities from deep-sea fungus, Aspergillus sydowi YH11-2. Arch Pharm Res 30: 1051-1054.
40. Li D, Wang F, Cai S, Zeng X, Xiao X, Gu Q, Zhu W (2007b) Two new bisorbicillinoids isolated from a deep-sea fungus, Phialocephala sp. FL30r. J Antibiot 60: 317-320.
41. Li D, Wang F, Xiao X, Zeng X, Gu Q, Zhu W (2007c) A new cytotoxic phenazine derivative from a deep sea bacterium Bacillus sp. Arch Pharm Res 30: 552-555.
42. Li Y, Ye D, Chen X, Lu X, Shao Z, Zhang H, Che Y (2009) Breviane spiroditerpenoids from an extreme-tolerant Penicillium sp. isolated from a deep sea sediment sample. J Nat Prod 72: 912-916.
43. López-García P, Philippe H, Gail F, Moreira D (2003) Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge. PNAS 100: 697-702.
44. Mancuso Nichols CA, Guezennec J, Bowman JP (2005) Bacterial exopolysaccharides from extreme marine environments with special consideration of the Southern Ocean, sea ice, and deep-sea hydrothermal vents: a review. Mar Biotech 7: 253-271.
45. Mathur EJ, Toledo G, Green BD, Podar M, Richardson TH, Kulwiec M, Chang HW (2005) A biodiversity-based approach to development of performance enzymes. Indus Biotech 1: 283-287.
46. Matou S, Colliec-Jouault S, Galy-Fauroux I, Ratiskol J, Sinquin C, Guezennec J, Fischer A-M, Helley D (2005) Effect of an oversulfated exopolysaccharide on angiogenesis induced by fibroblast growth factor-2 or vascular endothelial growth factor in vitro. Biochem Pharmacol 69: 751-759.
47. Molinski T, Dalisay DS, Lievens SL, Saludes JP (2009) Drug development from marine natural products. Nat Rev 8: 69-85.
48. Nakagawa S, Takai K (2008) Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance. FEMS Microbiol Ecol 65: 1-14.
49. Nakagawa S, Inagaki F, Takai K, Horikoshi K, Sako Y (2005a) Thioreductor micantisoli gen. nov., sp. nov., a novel mesophilic, sulfur-reducing chemolithoautotroph within the ε-Proteobacteria isolated from hydrothermal sediments in the Mid-Okinawa Trough. Int J Syst Evol Microbiol 55: 599-605.
50. Nakagawa S, Takai K, Inagaki F, Hirayama H, Nunoura T, Horikoshi K, Sako Y (2005b) Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field. Environ Microbiol 7: 1619-1632.
51. ε-Proteobacteria isolated from a deep-sea hydrothermal system in the Mid-Okinawa Trough. Int J Syst Evol Microbiol 55: 925-933.
52. Nunoura T, Miyazaki M, Suzuki Y, Takai K, Horikoshi K (2008) Hydrogenivirga okinawensis sp. nov., a thermophilic sulfur-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal field, Southern Okinawa Trough. Int J Syst Evol Microbiol 58: 676-681.
53. 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. Anton van Leeuwen 95: 121-133.
54. Park HB, Kwon HC, Lee C-H, Yang HO (2009) Glionitrin A, an antibiotic-antitumor metabolite derived from competitive interaction between abandoned mine microbes. J Nat Prod 72: 248-252.
55. Pathom-aree W, Stach JEM, Ward AC, Horikoshi K, Bull AT, Goodfellow M (2006) Diversity of actinomycetes isolated from Challenger Deep sediment (10, 898 m) from the Mariana Trench. Extremophiles 10: 181-189.
56. Pikuta EV, Marsic D, Itoh T, Bej AK, Tang J, Whitman WB, Ng JD, Garriott OK, Hoover RB (2007) Thermococcus thioreducens sp. nov., a novel hyperthermophilic, obligately sulfur-reducing archaeon from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 57: 1612-1618.
57. Raghukumar C, Mohandass C, Cardigos F, D'Costa PM, Santos RS, Colaco A (2008) Assemblage of benthic diatoms and culturable heterotrophs in shallow-water hydrothermal vent of the D. João de Castro Seamount, Azores in the Atlantic Ocean. Curr Sci 95: 1715-1723.
58. Raguénès G, Pignet P, Gauthier G, Peres A, Christen R, Rougeaux H, Barbier G, Guezennec J (1996) Description of a new polymer-secreting bacterium from a deep-sea hydrothermal vent, Alteromonas macleodii subsp. fijiensis, and preliminary characterization of the polymer. Appl Environ Microbiol 62: 67-73.
59. Raguénès G, Christen R, Guezennec J, Pignet P, Barbier G (1997a) Vibrio diabolicus sp. nov., a new polysaccharide-secreting organism isolated from a deep-sea hydrothermal vent polychaete annelid, Alvinella pompejana. Intl J Syst Bacteriol 47: 989-995.
60. Raguénès GHC, Peres A, Ruimy R, Pignet P, Christen R, Loaec M, Rougeaux H, Barbier G, Guezennec JG (1997b) Alteromonas infernus sp. nov., a new polysaccharide-producing bacterium isolated from a deep-sea hydrothermal vent. J Appl Microbiol 82: 422-430.
61. Rathgeber C, Yurkova N, Stackebrandt E, Schumann P, Humphrey E, Beatty JT, Yurkov V (2006) Metalloid reducing bacteria isolated from deep ocean hydrothermal vents of the Juan de Fuca Ridge, Pseudoalteromonas telluritireducens sp. nov. and Pseudoalteromonas spiralis sp. nov. Curr Microbiol 53: 449-456.
62. Reysenbach AL, Liu Y, Banta AB, Beveridge TJ, Kirshtein JD, Schouten S, Tivey MK, Von Damm KL, Voytek MA (2006) A ubiquitous thermoacidophilic archaeon from deep-sea hydrothermal vents. Nature 442: 444-447.
63. Schumacher RW, Davidson BS, Montenegro DA, Bernan VS (1995) γ-Indomycinone, a new pluramycin metabolite from a deep-sea derived actinomycete. J Nat Prod 58: 613-617.
64. Simon-Colin C, Raguénès G, Cozien J, Guezennec JG (2008) Halomonas profundus sp. nov., a new PHA-producing bacterium isolated from a deep-sea hydrothermal vent shrimp. J Appl Microbiol 104: 1425-1432.
65. Singh R, Sharma M, Joshi P, Rawat DS (2008) Clinical status of anti-cancer agents derived from marine sources. Anti-Canc Agents in Med Chem 8: 603-617.
66. Skropeta D (2008) Deep-sea natural products. Nat Prod Rep 25: 1131-1166.
67. Slobodkina GB, Kolganova TV, Tourova TP, Kostrikina NA, Jeanthon C, Bonch-Osmolovskaya EA, Slobodkin AI (2008) Clostridium tepidiprofundi sp. nov., a moderately thermophilic bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 58: 852-855.
68. Smith JL, Campbell BJ, Hanson TE, Zhang CL, Cary SC (2008) Nautilia profundicola sp. nov., a thermophilic, sulfur-reducing epsilonproteobacterium from deep-sea hydrothermal vents. Int J Syst Evol Microbiol 58: 1598-1602.
69. 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 underexplored "rare biosphere". PNAS 103: 12115-12120.
70. Stierle AA, Stierle DB, Goldstein E, Parker K, Bugni T, Baarson C, Gress J, Blake D (2003) A novel 5-HT receptor ligand and related cytotoxic compounds from an acid mine waste extremophiles. J Nat Prod 66: 1097-1100.
71. Stierle DB, Stierle AA, Hobbs JD, Stokken J, Clardy J (2004) Berkeleydione and berkeleytrione, new bioactive metabolites from an acid mine organism. Org Lett 6: 1049-1052.
72. Stierle AA, Stierle DB, Kelly K (2006) Berkelic acid, a novel spiroketal with selective anticancer activity from an acid mine waste fungal extremophile. J Org Chem 71: 5357-5360.
73. Stierle DB, Stierle AA, Patacini B (2007) The berkeleyacetals, three meroterpenes from a deep water acid mine waste Penicillium. J Nat Prod 70: 1820-1823.
74. van Dover CL, Lichtwardt RW (1986) A new trichomycete commensal with a galatheid squat lobster from deep-sea hydrothermal vents. Biol Bull 171: 461-468.
75. van Dover CL, German CR, Speer KG, Parson LM, Vrijenhoek RC (2002) Evolution and biogeography of deep-sea vent and seep invertebrates. Science 295: 1253-1257.
76. van Dover CL, Ward ME, Scott JL, Underdown J, Anderson B, Gustafson C, Whalen M, Carnegie RB (2007) A fungal epizootic in mussels at a deep-sea hydrothermal vent. Mar Ecol 28: 54-62.
77. Voordeckers JW, Do MY, Hügler M, Ko V, Sievert SM, Vetriani C (2008) Cultural dependent and independent analyses of 16S rRNA and ATP citrate lyase genes: a comparison of microbial communities from different black smoker chimneys on the Mid-Atlantic Ridge. Extremophiles 12: 627-640.
78. Wang F, Zhou H, Meng J, Peng X, Jiang L, Sun P, Zhang C, van Nostrand JD, Deng Y, He Z, Wu L, Zhou J, Xiao X (2009) GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. PNAS 106: 4840-4845.
79. Wilson ZE, Brimble MA (2009) Molecules derived from the extremes of life. Nat Prod Rep 26: 44-71.
80. Zanchetta P, Lagarde N, Guezennec J (2003) A new bone-healing material: a hyaluronic acid-like bacterial exopolysaccharide. Calcif Tiss Int 72: 74-79.
81. Zappa S, Rolland J-L, Flament D, Gueguen Y, Boudrant J, Dietrich J (2001) Characterization of a highly thermostable alkaline phosphatase from the euryarchaeon Pyrococcus abyssi. Appl Environ Microb 67: 4504-4511.