Bioprospection of marine microorganisms: Biotechnological applications and methods;Bioprospección de microorganismos marinos: Aplicaciones biotecnológicas y métodos

Revista Argentina de Microbiologia

Volumn 44, Issue 1, 2012, Pages 49-60

  Dionisi, Hebe M ^a   Lozada, Mariana ^a   Olivera, Nelda L ^a  

^a CENTRO NACIONAL PATAGÓNICO   (Argentina)

Author keywords

Argentina; Bioprospection; Biotechnological applications; Marine microorganisms

Indexed keywords

ANTHELMINTIC AGENT; ANTIBIOTIC AGENT; ANTINEOPLASTIC AGENT; HYDROXYMETHYLGLUTARYL COENZYME A REDUCTASE INHIBITOR; IMMUNOSUPPRESSIVE AGENT; PENICILLIN DERIVATIVE;

ACTINOBACTERIA; AGRICULTURAL MANAGEMENT; BACILLUS SUBTILIS; BACILLUS THURINGIENSIS; BIOCATALYSIS; BIOTECHNOLOGY; ENVIRONMENTAL MANAGEMENT; FLUORESCENCE MICROSCOPY; GENOMICS; MARINE SPECIES; METAGENOMICS; MICROBIOLOGICAL EXAMINATION; NONHUMAN; PHARMACY; PSEUDOMONAS FLUORESCENS; REVIEW; SPECIES CULTIVATION; WASTE WATER; WATER QUALITY; AGRICULTURAL INOCULATION; ARGENTINA; BIODIVERSITY; DRUG DEVELOPMENT; ECOSYSTEM; MARINE BIOLOGY; METHODOLOGY; MICROBIAL CONSORTIUM; MICROBIOLOGY;

AGRICULTURAL INOCULANTS; ARGENTINA; BIOCATALYSIS; BIODIVERSITY; BIOTECHNOLOGY; DRUG DISCOVERY; ECOSYSTEM; ENVIRONMENTAL MICROBIOLOGY; INDUSTRIAL MICROBIOLOGY; MARINE BIOLOGY; METAGENOMICS; MICROBIAL CONSORTIA;

EID: 84863751864     PISSN: 03257541     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (100)

1. Aakvik T, Degnes KF, Dahlsrud R, Schmidt F, Dam R, Yu L, Volker U, Ellingsen TE, Valla S. A. Plasmid RK2-based broad-host-range cloning vector useful for transfer of metagenomic libraries to a variety of bacterial species. FEMS Microbiol Lett 2009; 296: 149-58.
2. Adesemoye A, Kloepper J. Plant-microbes interactions in enhanced fertilizer-use efficiency. Appl Microbiol Biotechnol 2009; 85: 1-12.
3. Allen MJ, Jaspars M. Realizing the potential of marine biotechnology: challenges & opportunities. Ind Biotechnol 2009; 5: 77-83.
4. Arrieta JM, Arnaud-Haond S, Duarte CM. What lies underneath: conserving the oceans' genetic resources. Proc Natl Acad Sci U S A 2010; 107: 18318-24.
5. Bayer TS, Widmaier DM, Temme K, Mirsky EA, Santi DV, Voigt CA. Synthesis of methyl halides from biomass using engineered microbes. J Am Chem Soc 2009; 131: 6508-15.
6. Berg G. Plant-microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture. Appl Microbiol Biotechnol 2009; 84: 11-8.
7. Bernstein JR, Bulter T, Shen CR, Liao JC. Directed evolution of ribosomal protein S1 for enhanced translational efficiency of high GC Rhodopseudomonas palustris DNA in Escherichia coli. J Biol Chem 2007; 282: 18929-36.
8. Capon R. Australian microbial biodiscovery: from bugs to drugs. Microbiology Australia 2010; 75: 74.
9. Connon SA, Giovannoni SJ. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 2002; 68: 3878-85.
10. Chisti Y. Biodiesel from microalgae beats bioethanol. Trends Biotechnol 2008; 26: 126-31.
11. Chu X, He H, Guo C, Sun B. Identification of two novel esterases from a marine metagenomic library derived from South China Sea. Appl Microbiol Biotechnol 2008; 80: 615-25.
12. de Nys R, Steinberg PD. Linking marine biology and biotechnology. Curr Opin Biotechnol 2002; 13: 244-8.
13. Demain AL, Sanchez S. Microbial drug discovery: 80 years of progress. J Antibiot 2009; 62: 5-16.
14. Deming JW. Deep ocean environmental biotechnology. Curr Opin Biotechnol 1998; 9: 283-7.
15. Egan S, Thomas T, Kjelleberg S. Unlocking the diversity and biotechnological potential of marine surface associated microbial communities. Curr Opin Microbiol 2008; 11: 219-25.
16. Feller G, Le Bussy O, Gerday C. Expression of psychrophilic genes in mesophilic hosts: assessment of the folding state of a recombinant alpha-amylase. Appl Environ Microbiol 1998; 64:1163-5.
17. Ferrer M, Beloqui A, Timmis KN, Golyshin PN. Metagenomics for mining new genetic resources of microbial communities. J Mol Microbiol Biotechnol 2009; 16: 109-23.
18. Ferrer M, Golyshina O, Beloqui A, Golyshin PN. Mining enzymes from extreme environments. Curr Opin Microbiol 2007; 10:207-14.
19. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, McKenney K, Sutton GG, FitzHugh W, Fields CA, Gocayne JD, Scott JD, Shirley R, Liu LI, Glodek A, Kelley JM, Weidman JF, Phillips CA, Spriggs T, Hedblom E, Cotton MD, Utterback T, Hanna MC, Nguyen DT, Saudek DM, Brandon RC, Fine LD, Fritchman JL, Fuhrmann JL, Geoghagen NS, Gnehm CL, McDonald LA, Small KV, Fraser CM, Smith HO, Venter JC. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995; 269: 496-512.
20. Fu C, Hu Y, Xie F, Guo H, Ashforth E, Polyak S, Zhu B, Zhang L. Molecular cloning and characterization of a new cold-active esterase from a deep-sea metagenomic library. Appl Microbiol Biotechnol 2011; 90: 961-70.
21. Gabor EM, Alkema WB, Janssen DB. Quantifying the accessibility of the metagenome by random expression cloning techniques. Environ Microbiol 2004; 6: 879-86.
22. Gavrish E, Bollmann A, Epstein S, Lewis K. A trap for in situ cultivation of filamentous actinobacteria. J Microbiol Methods 2008; 72: 257-62.
23. Gilbert JA, Dupont CL. Microbial Metagenomics: Beyond the Genome. Ann Rev Mar Sci 2011; 3: 347-71.
24. Gupta M, Raghava S. Relevance of chemistry to white biotechnology. Chem Cent J 2007; 1:17.
25. Hårdeman F, Sjöling S. Metagenomic approach for the isolation of a novel low-temperature-active lipase from uncultured bacteria of marine sediment. FEMS Microbiol Ecol 2007; 59: 524-34.
26. Hatti-Kaul R, Törnvall U, Gustafsson L, Börjesson P. Industrial biotechnology for the production of bio-based chemicals - a cradle-to-grave perspective. Trends Biotechnol 2007; 25:119-24.
27. Heidelberg KB, Gilbert JA, Joint I. Marine genomics: at the interface of marine microbial ecology and biodiscovery. Microb Biotechnol 2010; 3: 531-43.
28. Hinde R, Pironet F, Borowitzka MA. Isolation of Oscillatoria spongeliae, the filamentous cyanobacterial symbiont of the marine sponge Dysidea herbacea. Marine Biology 1994; 119:99-104.
29. Hu Y Fu C, Huang Y, Yin Y, Cheng G, Lei F, Lu N, Li J, Ashforth EJ, Zhang L, Zhu B. Novel lipolytic genes from the microbial metagenomic library of the South China Sea marine sediment. FEMS Microbiol Ecol 2010; 72: 228-37.
30. Huse SM, Dethlefsen L, Huber JA, Welch DM, Relman DA, Sogin ML. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet 2008; 4: e1000255.
31. Ingham CJ, Sprenkels A, Bomer J, Molenaar D, van den Berg A, van Hylckama Vlieg JE, de Vos WM. The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms. Proc Natl Acad Sci U S A 2007; 104: 18217-22.
32. Jeon JH, Kim JT, Kim YJ, Kim HK, Lee HS, Kang SG, Kim SJ, Lee JH. Cloning and characterization of a new cold-active lipase from a deep-sea sediment metagenome. Appl Microbiol Biotechnol 2009; 81: 865-74.
33. Joint I, Muhling M, Querellou J. Culturing marine bacteria -an essential prerequisite for biodiscovery. Microb Biotechnol 2010;3:564-75.
34. Kaeberlein T, Lewis K, Epstein SS. Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science 2002; 296: 1127-9.
35. Kennedy J, Marchesi J, Dobson A. Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments. Microb Cell Fact 2008; 7:27.
36. Keshavarz T, Roy I. Polyhydroxyalkanoates: bioplastics with a green agenda. Curr Opin Microbiol 2010; 13: 321-6.
37. Kopke B, Wilms R, Engelen B, Cypionka H, Sass H. Microbial diversity in coastal subsurface sediments: a cultivation approach using various electron acceptors and substrate gradients. Appl Environ Microbiol 2005; 71: 7819-30.
38. Kyrpides NC. Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream. Nat Biotechnol 2009; 27: 627-32.
39. Lagesen K, Ussery DW, Wassenaar TM. Genome update: the 1000th genome - a cautionary tale. Microbiology 2010; 156:603-8.
40. Laport M, Santos O, Muricy G. Marine sponges: potential sources of new antimicrobial drugs. Curr Pharm Biotechnol 2009; 10:86-105.
41. Lee AK, Lewis DM, Ashman PJ. Microbial flocculation, a potentially low-cost harvesting technique for marine microalgae for the production of biodiesel. J Appl Phycol 2009;21:559-67.
42. Lee HS, Kwon KK, Kang SG, Cha SS, Kim SJ, Lee JH. Approaches for novel enzyme discovery from marine environments. Curr Opin Biotechnol 2010; 21: 353-7.
43. Lee M-H, Lee C-H, Oh T-K, Song JK, Yoon J-H. Isolation and characterization of a novel lipase from a metagenomic library of tidal flat sediments: evidence for a new family of bacterial lipases. Appl Environ Microbiol 2006; 72: 7406-9.
44. Lewis K, Epstein S, D'Onofrio A, Ling LL. Uncultured microorganisms as a source of secondary metabolites. J Antibiot 2010; 1-9.
45. Li Q, Du W, Liu D. Perspectives of microbial oils for biodiesel production. Appl Microbiol Biotechnol 2008; 80: 749-56.
46. Lozupone CA, Knight R. Global patterns in bacterial diversity. Proc Natl Acad Sci U S A 2007; 104: 11436-40.
47. Maldonado L, Stach J, Pathom-aree W, Ward A, Bull A, Goodfellow M. Diversity of cultivable actinobacteria in geographically widespread marine sediments. Antonie van Leeuwenhoek 2005; 87: 11-8.
48. McKew BA, Taylor JD, McGenity TJ, Underwood GJC. Resistance and resilience of benthic biofilm communities from a temperate saltmarsh to desiccation and rewetting. The ISME journal 2011; 5: 30-41.
49. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010; 11: 31-46.
50. Meyer H-P, Turner NJ. Biotechnological manufacturing options for organic chemistry. Mini Rev Org Chem 2009; 6: 300-6.
51. Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics 2010; 95: 315-27.
52. Morrissey J, Dow J, Mark G, O'Gara F. Are microbes at the root of a solution to world food production? EMBO Reports 2004; 5: 922.
53. Munn C. Marine microbiology: ecology and applications. London, BIOS Scientific Publ, 2004, 282 p.
54. Neumann H, Neumann-Staubitz P. Synthetic biology approaches in drug discovery and pharmaceutical biotechnology. Appl Microbiol Biotechnol 2010; 87: 75-86.
55. Nichols D, Cahoon N, Trakhtenberg EM, Pham L, Mehta A, Belanger A, Kanigan T, Lewis K, Epstein SS. Use of ichip for high-throughput in situ cultivation of "uncultivable" microbial species. Appl Environ Microbiol 2010; 76: 2445-50.
56. Nichols D, Lewis K, Orjala J, Mo S, Ortenberg R, O'Connor P, Zhao C, Vouros P, Kaeberlein T, Epstein SS. Short peptide induces an "uncultivable" microorganism to grow in vitro. Appl Environ Microbiol 2008; 74: 4889-97.
57. Ono A, Miyazaki R, Sota M, Ohtsubo Y, Nagata Y, Tsuda M. Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches. Appl Microbiol Biotechnol 2007; 74: 501-10.
58. Penesyan A, Marshall-Jones Z, Holmstrom C, Kjelleberg S, Egan S. Antimicrobial activity observed among cultured marine epiphytic bacteria reflects their potential as a source of new drugs. FEMS Microbiol Ecol 2009; 69: 113-24.
59. Querellou J, Borresen T, Boyen C, Dobson A, Hofle M, lanora A, Jaspars M, Kijjoa A, Olafsen J, Rigos G. Marine biotechnology: a new vision and strategy for Europe. ESF Marine Board Position Paper 2010; 15: 93.
60. Rahman H, Austin B, Mitchell WJ, Morris PC, Jamieson DJ, Adams DR, Spragg AM, Schweizer M. Novel anti-infective compounds from marine bacteria. Mar Drugs 2010; 8: 498.
61. Rappe MS, Connon SA, Vergin KL, Giovannoni SJ. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 2002; 418: 630-3.
62. Rappe MS, Giovannoni SJ. The uncultured microbial majority. Annu Rev Microbiol 2003; 57: 369-94.
63. Riesenfeld CS, Goodman RM, Handelsman J. Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ Microbiol 2004; 6: 981-9.
64. Rittmann BE. Microbial ecology to manage processes in environmental biotechnology. Trends Biotechnol 2006; 24: 261-6.
65. Rittmann B, Hausner M, Loffler F, Love N, Muyzer G, Okabe S, Oerther D, Peccia J, Raskin L, Wagner M. A vista for microbial ecology and environmental biotechnology. Environ Sci Technol 2006; 40:1096-103.
66. Rodriguez J, Lema JM, Kleerebezem R. Energy-based models for environmental biotechnology. Trends Biotechnol 2008; 26: 366-74.
67. Rogers AD, Laffoley DA. International Earth system expert workshop on ocean stresses and impacts. Summary report, 2011; IPSO Oxford, 18 pp.
68. Röling WFM, Ferrer M, Golyshin PN. Systems approaches to microbial communities and their functioning. Curr Opin Biotechnol 2010;21:532-8.
69. Sarkar S, Saha M, Roy D, Jaisankar P, Das S, Gauri Roy L, Gachhui R, Sen T, Mukherjee J. Enhanced production of antimicrobial compounds by three salt-tolerant actinobac-terial strains isolated from the Sundarbans in a niche-mimic bioreactor. Mar Biotechnol 2008; 10: 518-26.
70. Satpute SK, Banat IM, Dhakephalkar PK, Banpurkar AG, Chopade BA. Biosurfactants, bioemulsifiers and exopoly-saccharides from marine microorganisms. Biotechnol Adv 2010;28:436-50.
71. Schmidt EW. From chemical structure to environmental biosynthetic pathways: navigating marine invertebrate-bacteria associations. Trends Biotechnol 2005; 23: 437-40.
72. Schwarz S, Waschkowitz T, Daniel R. Enhancement of gene detection frequencies by combining DNA-based stable-isotope probing with the construction of metagenomic DNA libraries. World J Microbiol Biotechnol 2006; 22: 363-8.
73. Siegl A, Kamke J, Hochmuth T, Piel J, Richter M, Liang C, Dandekar T, Hentschel U. Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J 2011; 5: 61-70.
74. Simon C, Daniel R. Metagenomic analyses: past and future trends. Appl Environ Microbiol 2011; 77:1153-61.
75. Simon C, Herath J, Rockstroh S, Daniel R. Rapid identification of genes encoding DNA polymerases by function-based screening of metagenomic libraries derived from glacial ice. Appl Environ Microbiol 2009; 75: 2964-8.
76. Singh BK. Exploring microbial diversity for biotechnology: the way forward. Trends Biotechnol 2010; 28: 111-6.
77. Song J, Oh HM, Cho JC. Improved culturability of SAR11 strains in dilution-to-extinction culturing from the East Sea, West Pacific Ocean. FEMS Microbiology Letters 2009; 295: 141-7.
78. Song JS, Jeon JH, Lee JH, Jeong SH, Jeong BC, Kim SJ, Lee JH, Lee SH. Molecular characterization of TEM-type beta-lactamases identified in cold-seep sediments of Edison Seamount (south of Lihir Island, Papua New Guinea). J Microbiol 2005; 43: 172-8.
79. Tang WL, Zhao H. Industrial biotechnology: Tools and applications. Blotechnol J 2009; 4: 1725-39.
80. Tichet C, Nguyen HK, Yaakoubi SE, Bloch JF. Opinion: Commercial product exploitation from marine microbial biodiversity: some legal and IP issues. Microb Biotechnol 2010;3:507-13.
81. Trincone A. Marine biocatalysts: enzymatic features and applications. Mar Drugs 2011; 9: 478-99.
82. Tsueng G, Teisan S, Lam KS. Defined salt formulations for the growth of Salinispora tropica strain NPS21184 and the production of salinosporamide A (NPI-0052) and related analogs. Appl Microbiol Biotechnol 2008; 78: 827-32.
83. Uchiyama T, Abe T, Ikemura T, Watanabe K. Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat Biotech 2005; 23: 88-93.
84. Uchiyama T, Miyazaki K. Functional metagenomics for enzyme discovery: challenges to efficient screening. Curr Opin Biotechnol 2009; 20: 616-22.
85. Uchiyama T, Miyazaki K. Product-induced gene expression, a product-responsive reporter assay used to screen meta-genomic libraries for enzyme-encoding genes. Appl Environ Microbiol 2010; 76: 7029-35.
86. Uruburu F. History and services of culture collections. Int Microbiol 2003; 6: 101-3.
87. van Beuzekom B, Arundel A. OECD Biotechnology Statistics 2009. Paris, France.OECD Publishing 2009 103 p.
88. Van Lanen SG, Shen B. Microbial genomics for the improvement of natural product discovery. Curr Opin Microbiol 2006; 9: 252-60.
89. Verstraete W. Microbial ecology and environmental biotechnology. ISME J 2007; 1:4-8.
90. Warnecke F, Hess M. A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts. J Biotechnol 2009; 142: 91-5.
91. Warren RL, Freeman JD, Levesque RC, Smailus DE, Flibotte S, Holt RA. Transcription of foreign DNA in Escherichia coli. Genome Res 2008; 18: 1798-805.
92. Williamson LL, Borlee BR, Schloss PD, Guan C, Allen HK, Handelsman J. Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor. Appl Environ Microbiol 2005; 71: 6335-44.
93. Wohlgemuth R. The locks and keys to industrial biotechnology. New Biotechnology 2009; 25: 204-13.
94. Woyke T, Xie G, Copeland A, Gonzalez JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R. Assembling the marine metagenome, one cell at a time. PLoS One 2009; 4: e5299.
95. Wratschko K. Empirical Setting: The pharmaceutical industry. In: Strategic Orientation and Alliance Portfolio Configuration, Germany, Gabler Edition Wissenchaft, 2009 p.87-96.
96. Xu M, Xiao X, Wang F. Isolation and characterization of alkane hydroxylases from a metagenomic library of Pacific deep-sea sediment. Extremophiles 2008; 12: 255-62.
97. Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, Short JM, Keller M. Cultivating the uncultured. Proc Natl Acad SciUSA2002; 99: 15681-6.
98. Zengler K, Walcher M, Clark G, Haller I, Toledo G, Holland T, Mathur EJ, Woodnutt G, Short JM, Keller M. High-throughput cultivation of microorganisms using microcapsules. Methods Enzymol 2005; 397: 124-30.
99. Zhang C, Kim SK. Research and application of marine microbial enzymes: status and prospects. Mar Drugs 2010; 8: 1920-34.
100. Zhang H-Y, Chen L-L, Li X-J, Zhang J. Evolutionary inspirations for drug discovery. Trends Pharmacol Sci 2010; 31: 443-8.