Articles

EVALUATION OF THE METHODOLOGY IN MOLECULAR GEOMICROBIOLOGY

  • XIE Shu-cheng ,
  • YANG Jiao-yan ,
  • HUANG Jun-hua ,
  • LAI Xu-long ,
  • WANG Hong-mei
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  • 1.Biological Science and Technology,School of Environmental Studies, China University of Geosciences, Wuhan 430074,China;                        2.School of Earth Sciences, China University of Geosciences, Wuhan 430074,China;3.College of Life Sciences, Huazhong Normal University, Wuhan 430079,China

Received date: 2004-05-25

  Revised date: 2005-01-25

  Online published: 2005-06-25

Abstract

Microbes are extensively involved in geological processes occurring within a variety of ecosystems such as marine and oceans, lakes, soils, glaciers, caves, etc. Specific summaries of the microbial studies in individual ecosystems have been partly, if not wholly, presented in literatures. However, This paper overviews some advances in the studies of the biochemical components in molecular geomicrobiology, including nucleic acids (16S rRNA and DNA) and lipids (PLFA and hopanols). Summary is made on the lipid characteristics of specific geomicrobes. Typically, diplopterol, 2-methylhopanes and aryl isoprenoids (2-alkyl-1,3,4-trimethylbenzene) are respectively reviewed in the exploitation as the biomarkers of methanotrophs, cyanobacteria and green sulfur bacteria through the geological time. It is proposed that new techniques such as the integration of stable with radioactive isotopes of compoundspecific will enhance the further development of molecular geomicrobiology in the future.

Cite this article

XIE Shu-cheng , YANG Jiao-yan , HUANG Jun-hua , LAI Xu-long , WANG Hong-mei . EVALUATION OF THE METHODOLOGY IN MOLECULAR GEOMICROBIOLOGY[J]. Advances in Earth Science, 2005 , 20(6) : 664 -670 . DOI: 10.11867/j.issn.1001-8166.2005.06.0664

References

[1] Beerstecher E. Petroleum Microbiology [M]. New York: Elsevier, 1954.
[2] Kuznetsov S I, Inanov M V, Lyalikova M N. Introduction to Geomicrobiolgy (English translation)[M]. New York: McGrag-Hill,1963.
[3] Ehrlich H L. Geomicrobiolgy[M]. New York: Marcel Dekker, 2002.
[4] Newman D K, Banfield J F. Geomicrobiology: How molecular-scale interaction underpin biogeochemical systems[J].Science, 2002, 296:1 071-1 077.[5] Kasting J F, Siefert J L. Life and the evolution of Earth's atmosphere[J].Science, 2002, 296:1 066-1 068.
[6] Reysenbach A L, Shock E. Merging genomes with geochemistry in hydrothermal ecosystem[J].Science, 2002, 296:1 077-1 082.
[7] Edwards K J, Bond P L, Gihring T M,et al. An archaeal iron-oxidizing extreme acidophile important in acid mine drainage [J].Science, 2000, 287: 1 796-1 799.
[8] Northup D E, Lavoie K H. Geomicrobiolgy of caves: A review [J].Geomicrobiology Journal, 2001,18:199-222.
[9] Parkes R J, Cragg B A, Wellsbury P. Recent studies on bacterial populations and process in subseafloor sediments: A review [J].Hydrology Journal, 2000,8:11-28.
[10] Pancost R D, Damst J S S. Carbon isotopic compositions of prokaryotic lipids as tracers of carbon cycling in diverse settings [J].Chemical Geology,2003,195:29-58.
[11] Zhang Xiaojun, Ma Xiaojun, Yao Tandong, et al. Diversity of 16S rDNA and environmental factor influencing microorganisms in Malan ice core[J].Chinese Science Bulletin, 2003, 48(9):947-951.[张晓君,马晓军,姚檀栋,等.马兰冰芯16S rDNA的多样性与影响冰芯中微生物的环境因素[J].科学通报,2003,48(9):947-951.]
[12] Fish S A, Shepherd T J, McGenity T J, et al. Recovery of 16S ribosomal RNA gene fragments from ancient halite [J].Nature, 2002, 417 : 432-436.
[13] Macalady J, Banfield J F. Molecular geomicrobiology: Genes and geochemical cycling[J].Earth and Planetary Sciences Letters, 2003, 209:1-17.
[14] Chrestiner B C, Thompson E M, Thompson L G, et al. Recovery and identification of viable bacteria immured in glacial ice[J].Icarus, 2000,144:479-485.
[15] Dancer S J, Shears P, Platt D J. Isolation and characterization of coliforms from glacial ice and water in Canada's high Arctic[J].Journal of Applied Microbiology, 1997, 82:597-609.
[16] Ma L J, Catharine M C, Starmer W T, et al. Revival and characterization of fungi from ancient polar ice [J].Mycologist, 1999, 13:70-73.
[17] Zhang Xiaojun, Yao Tandong, Ma Xiaojun, et al. Analysis of the characteristics of microorganisms packed in the ice core of Malan Glacier, Tiber, China [J].Science in China(D), 2001, 44(suppl.):369-374.
[18] Llobet-Brossa E, Rossell -Mora R, Amann R. Microbial community composition of Wadden Sea sediments as revealed by fluorence in situ hybridization[J].Applied and Environmental Microbiology, 1998, 64:2 691-2 696.
[19] Ramsing N B, Fossing H, Ferdelmann T G, et al. Distribution of bacteria populations in a stratified fjord quatified by in situ hybridization and related to chemical gradients in the water column [J].Applied and Environmental Microbiology, 1996, 62:1 391-1 404.
[20] Felske A, Akkermans A D L, De Vos W M. In situ detection of an uncultured predominant Bacillus in dutch grassland soils [J].Applied and Environmental Microbiology, 1998, 64:4 588-4 590.
[21] Pennanen T, Frostegard A, Fritze H, et al. Phospholipid acid composition and heavy metal tolerance of soil microbial communities along two heavy metal-polluted gradients in Coniferous forest [J].Applied and Environmental Microbiology, 1996, 62(2): 420-428. 
[22] Fierer N, Schimel J P, Holden P A. Variation in microbial composition through two soil depth profiles [J].Soil & Biochemistry, 2003, 35: 167-176.
[23] Farriond P, Head I M, Innes E. Environmental influence on the biohopanoid composition of recent sediments [J].Geochimica et Cosmochimica, 2000, 64:2 985-2 992.
[24] Kelly J J, Häggblom M, Tate III R L. Changes in soil microbial communities over time resulting from one time application of zinc: A laboratory microcosm study [J].Soil Biology & Biochemistry,1999,31:1 455-1 465.
[25] Waldrop M P, Balser T C, Firestone M K. Linking microbial community composition to function in a tropical soil [J].Soil & Biochemistry, 2000, 32: 1 837-1 846.
[26] Petsch S T, Edwards K J, Eglinton T I. Abundance, distribution and δ13C analysis of microbial phospholipids-derived fatty acids in a black shale weathering profile[J].Organic Geochemistry, 2003, 34:731-743.
[27] Qi Hongyan, Xue Kai, Zhang Hongxun. Phospholipid fatty acid analysis and its application in microbial ecology[J].Acta Ecologica Sinica,2003,23(8):1 576-1 582.[齐鸿雁, 薛凯, 张洪勋.磷脂脂肪酸谱图分析方法及其在微生物生态学领域的应用[J].生态学报,2003,23(8):1 576-1 582.]
[28] Zhang Hanbo,Duan Changqun,Qu Lianghu. Culture independent methods for studies on microbial ecology of soils[J]. Chinese Journal of Ecology, 2003,22 (5):131-136.[张汉波,段昌群,屈良鹄.非培养方法在土壤微生物生态学研究中的应用[J].生态学杂志,2003,22(5):131-136.]
[29] Ourrison G, Albret P. Geohopanoids: The most abundant natural products on Earth? [J].Accounts of Chemistry Research, 1992, 25:398-402.
[30] Summons R E, Jahnke L L, Hope J M, et al. 2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis [J].Nature, 1999, 400:554-557.
[31] Pancost R D, Baas M, Damsté J S S. δ13C values and radiocarbon dates of microbial biomarkers as tracers for carbon recycling in peat deposits [J].Geology, 2000, 28: 663-666.
[32] Boschker H T S, Nold S C, Wellsbury P, et al. Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling biomarkers[J].Nature, 1998, 392:801-805.
[33] Hesselbo S P. Massive dissociation of gas hydrate a Jurassic oceanic event [J].Nature, 2000,406: 392-395.
[34] Hanson R S, Habson T E. Methanotrophic bacteria [J].Microbiology Review, 1996, 60:439-471.
[35] Bowman J P, Sly L I, Stacklebrandt E. The phylogenetic position of the family methylococcaceae [J].International Symposium on Bacteriology, 1993, 45:182-185.
[36] Freeman K H, Hayers J M, Trendel J M, et al. Evidence from carbon isotope measurements for diverse origins of sedimentary hydrocarbons [J].Nature, 1990, 343:254-256.
[37] Summons R E, Jahbke L L, Roksandic Z. Carbon isotopic fractionation in lipids from methanotrophic bacteria: Relevance for interpretation of the geochemical record of biomarkers [J]. Geochimica et Cosmochimica Acta, 1994, 58:2 853-2 863.
[38] Hinrichs U, Hayers M, Sylva S P, et al. Methane-consuming archaebacteria in marine sediments [J].Nature, 1999, 398: 802-805.
[39] Hinrichs K U. A molecular recorder of methane hydrate destabilization[J]. Geochemistry Geophysics Geosystems,2001, 2(1):2000GC0001 118.
[40] Rohmer M, Bouvier-Nave P, Ourisson G. Distribution of hopanoid triterpenes in prokaryotes [J].Journal of General Microbiology, 1984, 130:1 137-1 150.
[41] Hinrichs K U, Hmelo L, Sylva S P. Molecular fossils record of elevated methane levels in late Pleistocene coastal waters[J].Science, 2003, 229:1 214-1 217.
[42] Summons R E, Powell T G. Chlorobiaceae in Palaeozoic seas revealed by biological markers, isotopes and geology [J].Nature, 1986, 319:763-765.[43] Summons R E, Powell T G. Identification of aryl isoprenoids in source rocks and crude oils: Biological markers for the green sulphur bacteria[J]. Geochimica et Cosmochimica Acta,1987, 51:557-566.
[44] Yu K, Fan P, Philp R P. Novel biomarkers found in South Florida basin [J].Organic Geochemistry, 1990, 15:433-438. 
[45] Grice K, Schaeffer P, Schwark L, et al. Changes in palaeoenvironmental conditions during deposition of Permian Kupferschiefer (Lower Rhine Basin, northwest Germany) inferred from molecular and isotopic compositions of biomarker components[J].Organic Geochemistry, 1997, 26: 677-690.
[46] Sinninghe D J S, Kock-van D A C, de Leeuw J W. Identification of long-chain isoprenoid alkylbenzenes in sediments and crude oils [J].Geochimica et Cosmochimica Acta, 1988, 52:2 671-2 677.
[47] Simonin P, Jurgens U J, Rohmer M. Bacterial triterpenoids of the hopane series from the prochlorophyte Prochlorothrix hollandica and their intracellular localization[J].European Journal of Biochemistry, 1996, 241:865-871.
[48] Brocks J J, Logan G A, Buick R, et al. Archean molecular fossils and the early rise of eukaryotes [J].Science, 1999, 285:1 033-1 036.
[49] Finlay B J. Global dispersal of free-living microbial Eukaryote species [J].Science, 2002,296:1 061-1 063.
[50] Whitman W, Coleman D C, Wiebe W J. Prokaryotes: The unseen majority [J].Proceedings of the National Academy of Sciences USA, 1998, 95(12):6 578-6 583.
[51] Fenchel T. Microbial behavior in a heterogeneous world [J].Science, 2002, 296:1 068-1 071.
[52] Hilkert A W, Douthitt C B, Schluter H J, et al. Isotope ratio monitoring gas chromatography/mass spectrometry of D/H by high temperature conversion isotope ratio mass spectrometry [J].Rapid Communications in Mass Spectrometry,1999,13:1 226-1 230.

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