Molecular Biological Techniques in Geomicrobiology of Seafloor Hydrothermal Vents
Received date: 2009-01-15
Revised date: 2009-07-25
Online published: 2009-09-10
Recently, microbial ecology and related phenomena of seafloor hydrothermal vents have been the focus of geomicrobiology. Discoveries from these extreme environments continue to challenge accepted notions about microbial metabolism, limits of life and elemental geochemical cycles. Compared with traditional cultivation, phylogenetic analyses based on the small subunit rRNA (16S rRNA) and certain diagnostic metabolic genes have provided systematic and comprehensive methods to study microbial communities inhabited in hydrothermal chimneys. Cultivation-independent molecular techniques include construction of gene library, DGGE, T-RFLP, FISH and quantitative PCR. At present, these approaches have been successfully applied into the studies of geomicrobiology in global seafloor hydrothermal vents. Moreover, lots of achievements have also been accomplished in the investigations of microbial diversity, processes of key element geochemical cycles involved with microbes, the interactions between microbes and minerals, the origin of life and their evolution. In this review, we briefly outline the principles of various methods and their applications in research of microbial ecology of hydrothermal vents.
LI Jiang-Chao , ZHOU Fu-Yang , BANG Xiao-Tong , TUN Zi-Jun- . Molecular Biological Techniques in Geomicrobiology of Seafloor Hydrothermal Vents[J]. Advances in Earth Science, 2009 , 24(9) : 1015 -1023 . DOI: 10.11867/j.issn.1001-8166.2009.09.1015
[1] Corlis J B, Dymond J, Gordon L I, et al. Submarine thermal springs on the Galapagos Rift[J].Science,1979, 203: 1 073-1 083.
[2] Jannasch H W, Mottl M J. Geomicrobiology of deep-sea hydrothermal vents[J].Science,1985, 229: 717-725.
[3] Edwards K J, Bach W, McCollom T M. Geomicrobiology in oceanography: Microbe mineral interactions at and below the seafloor[J].TRENDS in Microbiology,2005, 13: 449-456.
[4] Kelley D S, Baross J A , Delaney J R. Volcanoes, fluids, and life at midocean ridge spreading centers[J].Annual Review of Earth and Planetary Sciences, 2001, 30: 385-491.
[5] Deming J W, Baross J A. Deep-sea smoker: Windows to a subsurface biosphere?[J].Geochimica et Cosmochimica Acta,1997, 57: 3 219-3 230.
[6] Edwards K J, McCollom T M, Konishi H, et al. Seafloor bioalteration of sulfide minerals: Results from in situ incubation studies[J].Geochimica et Cosmochimica Acta,2003, 67:2 843-2 856.
[7] Cowen J P. The microbial biosphere of sediment buried oceanic basement[J].Research of Microbiology,2004, 155: 497-506.
[8] Blöchl E, Rachel R, Burggraf S, et al. Pyrolobus fumarii, gen. and sp. nov., represents a novel group of archaea, extending the upper temperature limit for life to 113℃[J].Extremophiles, 1997, 1: 14-21.
[9] Kashefi K, Lovely D R. Extending the upper temperature limit for life[J].Science, 2003, 301: 934.
[10] Inagaki F,Takai K,Nealson K H,et al.Sulfurovum lithotrophicum gen. nov.,sp.nov.,a novel sulfur-oxidizing chemolithoautotroph within the epsilon-Proteobacteria isolated from the Okinawa Trough hydrothermal sediments[J].International Journal of Systematic and Evolutionary Microbiology,2004,54:1 477-1 482.
[11] Corre E, Reysenbach A-L, Prieur D. ε-Proteobacterial diversity from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge[J].FEMS Microbiology Letters, 2001, 205: 329-335.
[12] Hoek J, Banta A, Hubler F,et al. Microbial diversity of a sulphide spire located in the Edmond deep-sea hydrothermal vent filed on the Central Indian Ridge[J].Geobiology,2003,1:119-127.
[13] López-Garcia P, Duperron S, Philippot P, et al. Bacterial diversity in hydrothermal sediment and epsilon-proteobacterial dominance in experimental micro-colonizers at the Mid-Atlantic Ridge[J].Environmental Microbiology,2003, 5: 961-976.
[14] Kormas K A, Tivey M K, Damm K V, et al. Bacterial and archaeal phylotypes associated with distinct mineralogical layers of a white smoker spire from a deep-sea hydrothermal vent site[J].Environmental Microbiology, 2006, 8: 909-920.
[15] Ehrhardt C J,Haymon R M,Lamontagne M G,et al.Evidence for hydrothermal Archaea within the basaltic flanks of the East Pacific Rise[J].Environmental Microbiology,2007,9:900-912.
[16] Amann R I, Ludwig W, Schleifer K H. Phylogenetic identification and in situ detection of individualmicrobial cells without cultivation[J].Microbiology Reviews,1995, 59:143-169.
[17] Cary S C,Campbell B J,DeLong E F.Studying the deep subsurface biosphere: Emerging technologies and applications[C]//Wilcock W S D,DeLong E F,Kelley D S, et al,eds.The subseafloor biosphere at Mid-Ocean Ridges,Geophysical Monograph 144,American Geophysical Union.Washington DC,2004:383-399.
[18] Takai K, Nakagwa S, Reysenbach A-L, et al. Microbial ecology of mid-ocean ridges and back-arc basin[C]//Back-arc spreading systems: Geological biological, chemical, and physical interactions, Geophysical Monograph 166, American Geophysical Union. Washington DC,2004:185-213.
[19] Zhou J, Bruns M, Tiedje J. DNA recovery from soils of diverse composition[J].Applied and Environmental Microbiology,1996, 62: 316-322.
[20] Edwards K J, Bond P L, Gihring T M,et al. An archaea iron-oxidizing extreme acidophile important in acid mine drainage[J]. Science,2000,287:1 796-1 799.
[21] Page A, Tivey M K, Stakes D S, et al. Temporal and spatial archaeal colonization of hydrothermal vent deposits[J]. Environmental Microbiology,2008, 10:874-884.
[22] Tivey M K.Generation of seafloor hydrothermal vent fluids and associated mineral deposits[J].Oceanography,2007,20:50-65.[23] Woese C R, Fox G E. Phylogenetic structure of the Prokaryotic domain: the primary kingdom[J].Proceedings of the National Academy of Sciences,1977,74:5 088-5 090.
[24] Bult C J, White O, Olsen G J, et al. Complete genome sequence of the Methanogenic Archaea,Methanococcus Jannasehii[J].Science,1996, 273: 1058-1073.
[25] Corliss J B, Baross J A, Hoffman S E. A hypothesis concerning the relationship between submarine hot springs and the origin of life on Earth[J].Oceanologica Acta,1981,4:59-69.
[26] Nakagawa T, Nakagawa S, Inagaki F, et al. Phylogenetic diversity of sulfate-reducing prokaryotes in active deep-sea hydrothermal vent chimney structures[J].FEMS Microbiology Letters,2004, 232: 145-152.
[27] Dhillon A, Lever M, Lloyd K G, et al. Methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A (mcrA) genes in hydrothermal sediments of the Guaymas Basin[J].Applied and Environmental Microbiology, 2005, 71: 4 592-4 601.
[28] Brazelton W, Schrenk M, Kelley D, et al. Methane-and sulfur-metabolizing microbial communities dominate the Lost City hydrothermal field ecosystem[J].Applied and Environmental Microbiology, 2006, 72: 6 257-6 270.
[29] Schrenk M O, Kelley D S, Delaney J R, et al. Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney[J].Applied and Environmental Microbiology,2003, 69:3 580-3 592.
[30] Perner M, Kuever J, Seifert R, et al. The influence of ultramafic rocks on microbial communities at the Logatchev hydrothermal field, located 15°N on the Mid-Atlantic Ridge[J].FEMS Microbiology Ecology,2007, 61: 97-109.
[31] Takai K, Campbell B J, Cary S C, et al. Enzymatic and genetic characterization of carbon and energy metabolisms by deep-sea hydrothermal chemolithoautotrophic isolates of Epsilon-proteobacteria[J].Applied and Environmental Microbiology,2005, 71: 7 310-7 320.
[32] Fischer S G, Lerman L S. DNA fragments differing by single base pair substitutions are separated in Denaturing Gradient Gels: Correspondence with melting theory[J].Proceedings of the National Academy of Sciences,1983, 80: 1 579-1 583.
[33] Muyzer G, Teske A, Wirsen C O, et al. Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments[J].Archives of Microbiology, 1995, 164: 165-172.
[34] Yu Z T, Morrison M. Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by denaturing gradient gel electrophores[J].Applied and Environmental Microbiology,2004, 70: 4 800-4 806.
[35] Sievert S, Brinkhoff T, Muyzer G,et al.Spatial Heterogeneity of bacterial populations along an environmental gradient at a shallow submarine hydrothermal vent near Milos Island (Greece)[J].Applied and Environmental Microbiology,1999,65: 3 834-3 842.[36] Nakagawa T, Ishibashi J I, Maruyama A, et al. Analysis of Dissimilatory sulfite reductase and 16S rRNA gene fragments from deep-sea hydrothermal Sites of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific[J].Applied and Environmental Microbiology, 2004, 70: 393-403.
[37] Takai K, Komatus T, Inagaki F, et al. Distribution of archaea in a black smoker chimney structure[J].Applied and Environmental Microbiology,2001, 67:3 618-3 629.
[38] Taroncher-Oldenburg G, Francis C A, Ward B B. Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment[J].Applied and Environmental Microbiology, 2003, 69:1 159-1 171.
[39] Wang F P, Zhou H Y, Meng J, et al. GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent[J].Proceedings of the National Academy of Sciences,2009(in print).
[40] Pernthaler J, Glockner F O, Schonhuber W, et al. Fluorescence in situ hybridization with rRNA-targeted oligonucleotide probes[C]//Paul J H, ed. Methods in Microbiology: Marine Microbiology. New York:Academic Press, 2001:207-226.
[41] DeLong E F, Wickham G S, Pace N R. Phylogenetic stains: Ribosomal RNA based probes for the identification of single microbial cells[J].Science,1989, 243: 5 554-5 563.
[42] Orphan V, House C, Hinrichs K, et al. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis[J].Science,2001, 293: 484-487.
[43] Takai K, Oida H, Suzuki Y, et al. Spatial distribution of marine crenarchaeota group I in the vicinity of Deep-Sea hydrothermal Systems[J].Applied and Environmental Microbiology,2004, 70: 2 404-2 413.
[44] Taylor C D, Wirsen C O, Crail F. Rapid microbial production of filamentous sulfur mats at hydrothermal vents[J].Applied and Environmental Microbiology,1999, 65: 2 253-2 255.
[45] Peng X T, Zhou H Y, Yao H Q, et al. Microbe-related precipitation of iron and silica in the Edmond deep-sea hydrothermal vent field on the Central Indian Ridge[J].Chinese Science Bulletin,2007, 52: 3 233-3 238.
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