Genomics, metagenomics, and microbial oceanography-A sea of opportunities

Science China Earth Sciences

Volumn 54, Issue 4, 2011, Pages 473-480

  Fang, Jia Song ^a,b   Zhang, Li ^c  

^a Tongji University   (China)

^b HAWAII PACIFIC UNIVERSITY   (United States)

^c CHINA UNIVERSITY OF GEOSCIENCES   (China)

Author keywords

Archaea; Bacteria; Biogeochemistry; Biomass; Ecology; Ecosystem function; Eukarya; Genes; Genomics; Metabolism; Metagenomics; Microbial oceanography; Microbiology; Phylogeny; Physiology

Indexed keywords

ARCHAEA; ECOSYSTEM FUNCTION; EUKARYA; GENOMICS; METAGENOMICS; MICROBIAL OCEANOGRAPHY; PHYLOGENY;

BACTERIA; BACTERIOLOGY; BIOGEOCHEMISTRY; CLIMATE CHANGE; GENES; MARINE BIOLOGY; METABOLISM; OCEAN HABITATS; OCEANOGRAPHY; PHYSIOLOGY;

ECOSYSTEMS;

BIOGEOCHEMISTRY; BIOMASS; CARBON CYCLE; CLIMATE CHANGE; ECOSYSTEM FUNCTION; GENE; GENOMICS; MARINE ECOSYSTEM; METABOLISM; MICROBIAL ECOLOGY; MICROBIOLOGY; MICROORGANISM; PHYLOGENY; PHYSIOLOGY;

BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 79953685513     PISSN: 16747313     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11430-011-4179-0     Document Type: Review

References (80)

1. Karl D M. Microbial oceanography: Paradigms, processes and promise. Nature Rev Microbiol, 2007, 5: 759-769.
2. Karl D M, Proctor L M. Foundations of microbial oceanography. Oceanography, 2007, 16: 16-27.
3. Hallam S J, Mincer T J, Schleper C, et al. Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine crenarchaeota. PLoS Biol, 2006, 4: 0520-0536.
4. Doolittle W F, Papke R T. Genomics and the bacterial species problem. Genome Biol, 2006, 7: 116.
5. Venter J C, Remington K, Heidelberg J F, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science, 2004, 304: 66-74.
6. Pomeroy L R, Williams P J, Azam F, et al. The microbial loop. Oceanography, 2007, 20: 28-33.
7. Ducklow H W, Steinberg D K, Buesseler K O. Upper ocean carbon export and the biological pump. Oceanography, 2001, 14: 50-58.
8. Jiao N, Herndl G, Hansell D A, et al. Microbial production of recalcitrant dissolved organic matter: Long-term carbon storage in the global ocean. Nat Rev Microbiol, 2010, 8: 593-599.
9. Breitbart M, Thompson L R, Suttle C A, et al. Exploring the vast diversity of marine virus. Oceanography, 2007, 20: 135-139.
10. Rohwer F, Thurber R V. Marine viruses: Manipulating the marine environment. Nature, 2009, 459: 207-212.
11. Dickey T D. The emergence of concurrent high-resolution physical and bio-optical measurements in the upper ocean and their applications. Rev Geophys, 1991, 29: 383-413.
12. Helmreich S. Alien Ocean: Anthropological Voyages in Microbial Seas. Berkeley: University of California Press, 2009. 464.
13. Karl D M, Letelier R. Marine habitats and conditions for microbial growth. In: Schaechter M, ed. Encyclopedia of Microbiology. 3rd ed. Oxford: Elsevier, 2009. 258-277.
14. Chisholm S W. A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature, 1988, 334: 340-343.
15. Azam F, Malfatti F. Microbial structuring of marine ecosystems. Nat Rev Microbiol, 2007, 5: 782-791.
16. Herndl G J, Reinthaler T. The TRANSAT & ARCHIMEDES Shipboard Parties. Potential of Microbial Oceanography to Shed Light on the Dark Ocean's Enigmas. NIOZ Annual Report, 2008. http://www. nioz. nl/public/annual_report/2008/herndl. pdf.
17. Whitman W B, Coleman D C, Wiebe W J, et al. Prokaryotes: The unseen majority. Proc Natl Acad Sci USA, 1998, 95: 6578-6583.
18. Doney S, Abbott M, Cullen J, et al. From genes to ecosystems: The ocean's new frontier. Front Ecol Environ, 2004, 2: 457-466.
19. Aristegui J, Gasol J M, Duarte C M, et al. Microbial oceanography of the dark ocean's pelagic realm. Limn Oceanogr, 2009, 54: 1501-1529.
20. Lauro F M, Chastain R A, Blankenship L E, et al. The unique 16S rRNA genes of piezophiles reflect both phylogeny and adaptation. Appl Environ Microbiol, 2007, 73: 838-845.
21. Falkowski P, Scholes R J, Boyle E, et al. The global carbon cycle: A test of our knowledge of Earth as a system. Science, 2000, 290: 291-296.
22. Bowler C, Karl D, Colwell R. Microbial oceanography in a sea of opportunity. Nature, 2009, 459: 180-184.
23. Schlesinger W H. Biogeochemistry: An Analysis of Global Change. London: Academic Press, 1997. 588.
24. Strom S L. Microbial ecology of ocean biogeochemistry: A community perspective. Science, 2008, 320: 1043-1045.
25. Cullen J J, Doolittle W F, Levin S A, et al. Patterns and prediction in microbial oceanography. Oceanography, 2007, 20: 34-46.
26. Fuhrman J A. Microbial community structure and its functional implications. Nature, 2009, 459: 193-199.
27. Sogin M L, Morrison H G, Huber J A, et al. Micrboial diversity in the deep sea and the underexplored "rare biosphere." Proc Natl Acad Sci USA, 2006, 103: 12115-12120.
28. Fang J, Zhang L, Bazylinski D A. Deep-sea piezosphere and piezophiles: Geomicrobiology and biogeochemistry. Trends Microbiol, 2010, 18: 413-422.
29. Amann R I, Ludwig W, Schleifer K H, et al. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev, 1995, 59: 143-169.
30. Rappe M S, Giovannoni S J. The uncultured microbial majority. Annu Rev Microbiol, 2003, 57: 369-394.
31. Pace N R. A molecular view of microbial diversity and the biosphere. Science, 1997, 276: 734-740.
32. Giovannoni S, Stingl U. The importance of culturing bacterioplankton in the 'omics' age. Nature Rev Microbiol, 2007, 5: 820-826.
33. DeLong E F. Archaea in coastal marine environments. Proc Natl Acad Sci USA, 1992, 89: 5685-5689.
34. Fuhrman J A, McCallum K, Davis A A. Novel major archaebacterial group from marine plankton. Nature, 1992, 356: 148-149.
35. Massana R, Murray A E, Preston C M, et al. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara channel. Appl Environ Microbiol, 1997, 63: 50-56.
36. Karner M B, DeLong E F, Karl D M. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature, 2001, 409: 507-510.
37. Herndl G J, Reinthaler T, Teira E, et al. Contribution of archaea to total prokaryotic production in the deep Atlantic Ocean. Appl Environ Microbiol, 2005, 71: 2303-2309.
38. 14C analysis. Geochim Cosmochim Acta, 2001, 65: 3123-3137.
39. Könneke M, Bernhard A E, de la Torre J R, et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature, 2005, 437: 543-546.
40. Hallam S J, Konstantinidis K T, Putnam N, et al. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci USA, 2006, 103: 18296-18301.
41. Mincer T J, Church M J, Taylor L T, et al. Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ Microbiol, 2007, 9: 1162-1175.
42. Francis C A, Beman J M, Kuypersl M M M. New processes and players in the nitrogen cycle: The microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J, 2007, 1: 19-27.
43. DeLong E F. The microbial ocean from genomes to biomes. Nature, 2009, 459: 200-206.
44. Venter J C, Remington K, Heidelberg J F, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science, 2004, 304: 66-74.
45. Tringe S G, Von Mering C, Kobayashi A, et al. Comparative metagenomics of microbial communities. Science, 2005, 308: 554-557.
46. Tringe S G, Rubin E M. Metagenomics: DNA sequencing of environmental samples. Nature Rev Genetics, 2005, 6: 805-814.
47. Mou X, Sun S, Edwards R A, et al. Bacterial carbon processing by generalist species in the coastal ocean. Nature, 2008, 451: 708-714.
48. Kerkhof L J, Goodman R M. Ocean microbial metagenomics. Deep-Sea Res II, 2009, 56: 1824-1829.
49. Medini D, Serruto D, Parkhil J, et al. Microbiology in the post-genomic era. Nature Rev Microbiol, 2008, 6: 1-13.
50. Béjà O, Aravind L, Koonin E V, et al. Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. Science, 2000, 289: 1902-1906.
51. Giovannoni S J, Bibbs L, Cho J C, et al. Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature, 2005, 438: 82-85.
52. Gómez-Consarnau L, González J M, Coll-Lladó M, et al. Light stimulates growth of proteorhodopsin-containing marine flavobacteria. Nature, 2007, 445: 210-213.
53. Tripp H J, Bench S R, Turk K A, et al. Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium. Nature, 2010, 464: 90-94.
54. Jiao N Z, Zhang Y, Zeng Y, et al. Distinct distribution pattern of abundance and diversity of aerobic anoxygenic phototrophic bacteria in the global ocean. Environ Microbiol, 2007, 9: 3091-3099.
55. Jiao N, Zhang F, Hong N. Significant roles of bacteriochlorophylla supplemental to chlorophylla in the ocean. ISME J, 2009, 4: 595-597.
56. Cottrell M T, Ras J, Kirchman D L. Bacteriochlorophyll and community structure of aerobic anoxygenic phototrophic bacteria in a particle-rich estuary. ISME J, 2010, 4: 945-954.
57. DeLong E F, Preston C M, Mincer T, et al. Community genomics among stratified microbial assemblages in the ocean's interior. Science, 2006, 311: 496-503.
58. Martin-Cuadrado A B, López-García P, Alba J C, et al. Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS ONE, 2007, 2: e914.
59. Fang J, Zhang L. Explore the deep biosphere. Sci China-Earth Sci, 2011, 54: 157-165.
60. National Research Council. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington DC: The National Academies Press, 2008. 170.
61. Helmreich S. Alien Ocean: Anthropological Voyages in Microbial Seas. Berkeley: University of California Press, 2009. 464.
62. Tyson G W, Chapman J, Hugenholtz P, et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 2004, 428: 37-43.
63. DeLong E F, Karl D M. Genomic perspectives in microbial oceanography. Nature, 2005, 437: 336-342.
64. Frias-Lopez J, Shi Y, Tyson G W, et al. Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA, 2008, 105: 3805-3810.
65. Ingalls A E, Shah S R, Hansman R L, et al. Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. Proc Natl Acad Sci USA, 2006, 103: 6442-6447.
66. Neufeld J D, Wagner M, Murrell J C. Who eats what, where and when? Isotopelabelling experiments are coming of age. ISME J, 2007, 1: 103-110.
67. Shi Y, Tyson G W, DeLong E F. Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature, 2009, 459: 266-269.
68. Stingl U, Tripp H J, Giovannoni S J. Improvements of highthroughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site. ISME J, 2007, 1: 361-371.
69. Zengler K, Toledo G, Rappé M, et al. Cultivating the uncultured. Proc Natl Acad Sci USA, 2002, 99: 15681-15686.
70. Takai K, Miyazaki M, Hirayama H, et al. Isolation and physiological characterization of two novel, piezophilic, thermophilic chemolithoautotrophs from a deep-sea hydrothermal vent chimney. Environ Microbiol, 2009, 11: 1983-1997.
71. Kaeberlein T, Lewis K, Epstein S S. Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science, 2002, 296: 1127-1129.
72. Ferrari B C, Binnerup S J, Gillings M, et al. Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria. Appl Environ Microbiol, 2005, 71: 8714-8720.
73. Park H S, Schumacher R, Kilbane J J. New method to characterize microbial diversity using flow cytometry. J Ind Microbiol Biotechnol, 2005, 32: 94-102.
74. Lasken R S, Kvist T, Ishøy T, et al. Multiple Displacement Amplification from single bacterial cells. In: Hughes S, Lasken R, eds. Whole Genome Amplification. Banbury: Scion Publishing Ltd., 2005. 119-147.
75. Lasken R S. Single-cell genomic sequencing using multiple displacement amplification. Curr Opin Microbiol, 2007, 10: 510-516.
76. Walker A, Parkhill J. Single-cell genomics. Nat Rev Microbiol, 2008, 6: 176-177.
77. Siegl A, Kamke J, Hochmuth T, et al. Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J, 2011, 5: 61-70.
78. Woyke T, Tighe D, Mavromatis K, et al. One bacterial cell, one complete genome. PLoS ONE 2010, 5: e10314, doi: 10. 1371/journal. pone. 0010314.
79. Seshadri R, Kravitz S A, Smarr L, et al. CAMERA: A community resource for metagenomics. PLoS Biol, 2007, 5: e75.
80. Rothstein L, Cullen J, Abbott M, et al. Modeling ocean ecosystem: The PARADIGM program. Oceanography, 2006, 19: 22-51.