Skip to main content
Log in

Current molecular biologic techniques for characterizing environmental microbial community

  • Review Article
  • Published:
Frontiers of Environmental Science & Engineering Aims and scope Submit manuscript

Abstract

Microbes are vital to the earth because of their enormous numbers and instinct function maintaining the natural balance. Since the microbiology was applied in environmental science and engineering more than a century ago, researchers desire for more and more information concerning the microbial spatio-temporal variations in almost every fields from contaminated soil to wastewater treatment plant (WWTP). For the past 30 years, molecular biologic techniques explored for environmental microbial community (EMC) have spanned a broad range of approaches to facilitate the researches with the assistance of computer science: faster, more accurate and more sensitive. In this feature article, we outlined several current and emerging molecular biologic techniques applied in detection of EMC, and presented and assessed in detail the application of three promising tools.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Tiedje J, Donohue T. Microbes in the energy grid. Science, 2008, 320(5879): 985

    Article  CAS  Google Scholar 

  2. Lemaire R, Webb R I, Yuan Z G. Micro-scale observations of the structure of aerobic microbial granules used for the treatment of nutrient-rich industrial wastewater. ISME J, 2008, 2(5): 528–541

    Article  CAS  Google Scholar 

  3. Kartal B, Kuenen J G, van Loosdrecht M C M. Sewage treatment with anammox. Science, 2010, 328(5979): 702–703

    Article  CAS  Google Scholar 

  4. Xu M Y, Wu W M, Wu L Y, He Z L, van Nostrand J D, Deng Y, Luo J A, Carley J, Ginder-Vogel M, Gentry T J, Gu B H, Watson D, Jardine P M, Marsh T L, Tiedje J M, Hazen T, Criddle C S, Zhou J Z. Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation. ISME J, 2010, 4(8): 1060–1070

    Article  Google Scholar 

  5. Fuhrman J A. Microbial community structure and its functional implications. Nature, 2009, 459(7244): 193–199

    Article  CAS  Google Scholar 

  6. Hori T, Haruta S, Ueno Y, Ishii M, Igarashi Y. Dynamic transition of a methanogenic population in response to the concentration of volatile fatty acids in a thermophilic anaerobic digester. Applied and Environmental Microbiology, 2006, 72(2): 1623–1630

    Article  CAS  Google Scholar 

  7. Ikeda S, Rallos L E E, Okubo T, Eda S, Inaba S, Mitsui H, Minamisawa K. Microbial community analysis of field-grown soybeans with different nodulation phenotypes. Applied and Environmental Microbiology, 2008, 74(18): 5704–5709

    Article  CAS  Google Scholar 

  8. Wood S A, Rueckert A, Cowan D A, Cary S C. Sources of edaphic cyanobacterial diversity in the Dry Valleys of Eastern Antarctica. ISME J, 2008, 2(3): 308–320

    Article  CAS  Google Scholar 

  9. Kvennefors E C E, Sampayo E, Ridgway T, Barnes A C, Hoegh-Guldberg O. Bacterial communities of two ubiquitous Great Barrier Reef corals reveals both site- and species-specificity of common bacterial associates. PLOS ONE, 2010, 5(4):1–14

    Article  CAS  Google Scholar 

  10. Mikkelsen D, Kappler U, McEwan A G, Sly L I. Probing the archaeal diversity of a mixed thermophilic bioleaching culture by TGGE and FISH. Systematic and Applied Microbiology, 2009, 32(7): 501–513

    Article  CAS  Google Scholar 

  11. Xue D W, Feng S G, Zhao H Y, Jiang H, Shen B, Shi N N, Lu J J, Liu J J, Wang H Z. The linkage maps of Dendrobium species based on RAPD and SRAP markers. Journal of Genetics and Genomics = Yi Chuan Xue Bao, 2010, 37(3): 197–204

    CAS  Google Scholar 

  12. Rodas A M, Ferrer S, Pardo I. 16S-ARDRA, a tool for identification of lactic acid bacteria isolated from grape must and wine. Systematic and Applied Microbiology, 2003, 26(3): 412–422

    Article  CAS  Google Scholar 

  13. Deiglmayr K, Philippot L, Tscherko D, Kandeler E. Microbial succession of nitrate-reducing bacteria in the rhizosphere of Poa alpina across a glacier foreland in the Central Alps. Environmental Microbiology, 2006, 8(9): 1600–1612

    Article  CAS  Google Scholar 

  14. Alvarado P, Manjón J L. Selection of enzymes for terminal restriction fragment length polymorphism analysis of fungal internally transcribed spacer sequences. Applied and Environ-mental Microbiology, 2009, 75(14): 4747–4752

    Article  CAS  Google Scholar 

  15. Talbot G, Roy C S, Topp E, Beaulieu C, Palin M F, Massé D I. Multivariate statistical analyses of rDNA and rRNA fingerprint data to differentiate microbial communities in swine manure. FEMS Microbiology Ecology, 2009, 70(3): 540–552

    Article  CAS  Google Scholar 

  16. Chandler D P, Kukhtin A, Mokhiber R, Knickerbocker C, Ogles D, Rudy G, Golova J, Long P, Peacock A. Monitoring microbial community structure and dynamics during in situ U(VI) bioremediation with a field-portable microarray analysis system. Environmental Science & Technology, 2010, 44(14): 5516–5522

    Article  CAS  Google Scholar 

  17. Brulc J M, Antonopoulos D A, Berg Miller M E, Wilson M K, Yannarell A C, Dinsdale E A, Edwards R E, Frank E D, Emerson J B, Wacklin P, Coutinho PM, Henrissat B, Nelson K E, White B A. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proceedings of the National Academy of Sciences of the United States of America, 2009, 106(6): 1948–1953

    Article  CAS  Google Scholar 

  18. Mou X Z, Sun S L, Edwards R A, Hodson R E, Moran M A. Bacterial carbon processing by generalist species in the coastal ocean. Nature, 2008, 451(7179): 708–711

    Article  CAS  Google Scholar 

  19. Poitelon J B, Joyeux M, Welté B, Duguet J P, Prestel E, Lespinet O, DuBow M S. Assessment of phylogenetic diversity of bacterial microflora in drinking water using serial analysis of ribosomal sequence tags. Water Research, 2009, 43(17): 4197–4206

    Article  CAS  Google Scholar 

  20. Sahl J W, Schmidt R H, Swanner E D, Mandernack K W, Templeton A S, Kieft T L, Smith R L, Sanford W E, Callaghan R L, Mitton J B, Spear J R. Subsurface microbial diversity in deepgranitic-fracture water in Colorado. Applied and Environmental Microbiology, 2008, 74(1): 143–152

    Article  CAS  Google Scholar 

  21. Burkhardt E M, Akob D M, Bischoff S, Sitte J, Kostka J E, Banerjee D, Scheinost A C, Küsel K. Impact of biostimulated redox processes on metal dynamics in an iron-rich creek soil of a former uranium mining area. Environmental Science & Technology, 2010, 44(1): 177–183

    Article  CAS  Google Scholar 

  22. Foley M E, Sigler V, Gruden C L. A multiphasic characterization of the impact of the herbicide acetochlor on freshwater bacterial communities. ISME J, 2008, 2(1): 56–66

    Article  CAS  Google Scholar 

  23. Kim J M, Lee H J, Kim S Y, Song J J, Park W, Jeon C O. Analysis of the fine-scale population structure of “Candidatus accumulibacter phosphatis” in enhanced biological phosphorus removal sludge, using fluorescence in situ hybridization and flow cytometric sorting. Applied and Environmental Microbiology, 2010, 76(12): 3825–3835

    Article  CAS  Google Scholar 

  24. Hesselsoe M, Füreder S, Schloter M, Bodrossy L, Iversen N, Roslev P, Nielsen P H, Wagner M, Loy A. Isotope array analysis of Rhodocyclales uncovers functional redundancy and versatility in an activated sludge. ISME J, 2009, 3(12): 1349–1364

    Article  CAS  Google Scholar 

  25. White D C, Davis W M, Nickels J S, King J D, Bobbie R J. Determination of the sedimentary microbial biomass by extractible lipid phosphate. Oecologia, 1979, 40(1): 51–62

    Article  Google Scholar 

  26. Yergeau E, Bezemer T M, Hedlund K, Mortimer S R, Kowalchuk G A, van der Putten W H, Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils. Environmental Microbiology, 2010, 12(8): 2096–2106

    CAS  Google Scholar 

  27. Yao H Y, Wu F Z. Soil microbial community structure in cucumber rhizosphere of different resistance cultivars to fusarium wilt. FEMS Microbiology Ecology, 2010, 72(3): 456–463

    Article  CAS  Google Scholar 

  28. Schütz K, Nagel P, Vetter W, Kandeler E, Ruess L. Flooding forested groundwater recharge areas modifies microbial communities from top soil to groundwater table. FEMS Microbiology Ecology, 2009, 67(1): 171–182

    Article  CAS  Google Scholar 

  29. Björk R G, Ernfors M, Sikström U, Nilsson M B, Andersson M X, Rütting T, Klemedtsson L. Contrasting effects of wood ash application on microbial community structure, biomass and processes in drained forested peatlands. FEMS Microbiology Ecology, 2010, 73(3): 550–562

    Google Scholar 

  30. Wang MC, Liu Y H, Wang Q, Gong M, Hua XM, Pang Y J, Hu S, Yang Y H. Impacts of methamidophos on the biochemical, catabolic, and genetic characteristics of soil microbial communities. Soil Biology & Biochemistry, 2008, 40(3): 778–788

    Article  CAS  Google Scholar 

  31. Muyzer G, de Waal E C, Uitterlinden A G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology, 1993, 59(3): 695–700

    CAS  Google Scholar 

  32. Fromin N, Hamelin J, Tarnawski S, Roesti D, Jourdain-Miserez K, Forestier N, Teyssier-Cuvelle S, Gillet F, Aragno M, Rossi P. Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environmental Microbiology, 2002, 4(11): 634–643

    Article  CAS  Google Scholar 

  33. Hjort K, Bergström M, Adesina M F, Jansson J K, Smalla K, Sjöling S. Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil. FEMS Microbiology Ecology, 2010, 71(2): 197–207

    Article  CAS  Google Scholar 

  34. Parkes R J, Cragg B A, Banning N, Brock F, Webster G, Fry J C, Hornibrook E, Pancost R D, Kelly S, Knab N, Jørgensen B B, Rinna J, Weightman A J. Biogeochemistry and biodiversity of methane cycling in subsurface marine sediments (Skagerrak, Denmark). Environmental Microbiology, 2007, 9(5): 1146–1161

    Article  CAS  Google Scholar 

  35. Wang X H, Wen X H, Criddle C, Wells G, Zhang J, Zhao Y. Community analysis of ammonia-oxidizing bacteria in activated sludge of eight wastewater treatment systems. Journal of Environmental Sciences (China), 2010, 22(4): 627–634

    Article  CAS  Google Scholar 

  36. Suzuki M, Rappe MS, Giovannoni S J. Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Applied and Environmental Microbiology, 1998, 64(11): 4522–4529

    CAS  Google Scholar 

  37. Bulgari D, Casati P, Brusetti L, Quaglino F, Brasca M, Daffonchio D, Bianco P A. Endophytic bacterial diversity in grapevine (Vitis vinifera L.) leaves described by 16S rRNA gene sequence analysis and length heterogeneity-PCR. Journal of Microbiology (Seoul, Korea), 2009, 47(4): 393–401

    Article  CAS  Google Scholar 

  38. Ahn C, Peralta R M. Soil bacterial community structure and physicochemical properties in mitigation wetlands created in the Piedmont region of Virginia (USA). Ecological Engineering, 2009, 35(7): 1036–1042

    Article  Google Scholar 

  39. Taipale S, Jones R I, Tiirola M. Vertical diversity of bacteria in an oxygen-stratified humic lake, evaluated using DNA and phospholipid analyses. Aquatic Microbial Ecology, 2009, 55(1): 1–16

    Article  Google Scholar 

  40. Mills D K, Fitzgerald K, Litchfield C D, Gillevet P M. A comparison of DNA profiling techniques for monitoring nutrient impact on microbial community composition during bioremediation of petroleum-contaminated soils. Journal of Microbiological Methods, 2003, 54(1): 57–74

    Article  CAS  Google Scholar 

  41. Ritchie N J, Schutter M E, Dick R P, Myrold D D. Use of length heterogeneity PCR and fatty acid methyl ester profiles to characterize microbial communities in soil. Applied and Environmental Microbiology, 2000, 66(4): 1668–1675

    Article  CAS  Google Scholar 

  42. Tiirola M A, Suvilampi J E, Kulomaa M S, Rintala J A. Microbial diversity in a thermophilic aerobic biofilm process: analysis by length heterogeneity PCR (LH-PCR). Water Research, 2003, 37(10): 2259–2268

    Article  CAS  Google Scholar 

  43. Suzuki M T. Effect of protistan bacterivory on coastal bacterioplankton diversity. Aquatic Microbial Ecology, 1999, 20(3): 261–272

    Article  Google Scholar 

  44. Dorigo U, Volatier L, Humbert J F. Molecular approaches to the assessment of biodiversity in aquatic microbial communities. Water Research, 2005, 39(11): 2207–2218

    Article  CAS  Google Scholar 

  45. Fisher M M, Triplett E W. Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Applied and Environmental Microbiology, 1999, 65(10): 4630–4636

    CAS  Google Scholar 

  46. Manter D K, Delgado J A, Holm D G, Stong R A. Pyrosequencing reveals a highly diverse and cultivar-specific bacterial endophyte community in potato roots. Microbial Ecology, 2010, 60(1): 157–166

    Article  Google Scholar 

  47. Knief C, Ramette A, Frances L, Alonso-Blanco C, Vorholt J A. Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere. ISME J, 2010, 4(6): 719–728

    Article  CAS  Google Scholar 

  48. Ranjard L, Poly F, Lata J C, Mougel C, Thioulouse J, Nazaret S. Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Applied and Environmental Microbiology, 2001, 67(10): 4479–4487

    Article  CAS  Google Scholar 

  49. Sanz J L, Kochling T. Molecular biology techniques used in wastewater treatment: an overview. Process Biochemistry, 2007, 42(2): 119–133

    Article  CAS  Google Scholar 

  50. Brinkmeyer R, Knittel K, Jürgens J, Weyland H, Amann R, Helmke E. Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice. Applied and Environmental Microbiology, 2003, 69(11): 6610–6619

    Article  CAS  Google Scholar 

  51. Glöckner F O, Fuchs B M, Amann R. Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Applied and Environmental Microbiology, 1999, 65(8): 3721–3726

    Google Scholar 

  52. Knittel K, Lösekann T, Boetius A, Kort R, Amann R. Diversity and distribution of methanotrophic archaea at cold seeps. Applied and Environmental Microbiology, 2005, 71(1): 467–479

    Article  CAS  Google Scholar 

  53. Eilers H, Pernthaler J, Glöckner F O, Amann R. Culturability and In situ abundance of pelagic bacteria from the North Sea. Applied and Environmental Microbiology, 2000, 66(7): 3044–3051

    Article  CAS  Google Scholar 

  54. Schramm A, de Beer D, van den Heuvel J C, Ottengraf S, Amann R. Microscale distribution of populations and activities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifying bioreactor: quantification by in situ hybridization and the use of microsensors. Applied and Environmental Microbiology, 1999, 65(8): 3690–3696

    CAS  Google Scholar 

  55. Gieseke A, Purkhold U, Wagner M, Amann R, Schramm A. Community structure and activity dynamics of nitrifying bacteria in a phosphate-removing biofilm. Applied and Environmental Microbiology, 2001, 67(3): 1351–1362

    Article  CAS  Google Scholar 

  56. Altmann D, Stief P, Amann R, de Beer D. Distribution and activity of nitrifying bacteria in natural stream sediment versus laboratory sediment microcosms. Aquatic Microbial Ecology, 2004, 36(1): 73–81

    Article  Google Scholar 

  57. Ravenschlag K, Sahm K, Knoblauch C, Jørgensen B B, Amann R. Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine arctic sediments. Applied and Environmental Microbiology, 2000, 66(8): 3592–3602

    Article  CAS  Google Scholar 

  58. Llobet-Brossa E, Rabus R, Bottcher M E, Konneke M, Finke N, Schramm A, Meyer R L, Grotzschel S, Rossello-Mora R, Amann R. Community structure and activity of sulfate-reducing bacteria in an intertidal surface sediment: a multi-method approach. Aquatic Microbial Ecology, 2002, 29(3): 211–226

    Article  Google Scholar 

  59. Christensson M, Blackall L L, Welander T. Metabolic transformations and characterisation of the sludge community in an enhanced biological phosphorus removal system. Applied Microbiology and Biotechnology, 1998, 49(2): 226–234

    Article  CAS  Google Scholar 

  60. Strous M, Kuenen J G, Jetten MS M. Key physiology of anaerobic ammonium oxidation. Applied and Environmental Microbiology, 1999, 65(7): 3248–3250

    CAS  Google Scholar 

  61. Tran H T, Park Y J, Cho M K, Kim D J, Ahn D H. Anaerobic ammonium oxidation process in an upflow anaerobic sludge blanket reactor with granular sludge selected from an anaerobic digestor. Biotechnology and Bioprocess Engineering, 2006, 11(3): 199–204

    Article  CAS  Google Scholar 

  62. Miura Y, Watanabe Y, Okabe S. Significance of Chloroflexi in performance of submerged membrane bioreactors (MBR) treating municipal wastewater. Environmental Science & Technology, 2007, 41(22): 7787–7794

    Article  CAS  Google Scholar 

  63. Webster G, Blazejak A, Cragg B A, Schippers A, Sass H, Rinna J, Tang X H, Mathes F, Ferdelman T G, Fry J C, Weightman A J, Parkes R J. Subsurface microbiology and biogeochemistry of a deep, cold-water carbonate mound from the Porcupine Seabight (IODP Expedition 307). Environmental Microbiology, 2009, 11(1): 239–257

    Article  CAS  Google Scholar 

  64. Lee N, Nielsen P H, Andreasen K H, Juretschko S, Nielsen J L, Schleifer K H, Wagner M. Combination of fluorescent in situ hybridization and microautoradiography-a new tool for structurefunction analyses in microbial ecology. Applied and Environmental Microbiology, 1999, 65(3): 1289–1297

    CAS  Google Scholar 

  65. Ouverney C C, Fuhrman J A. Combined microautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ. Applied and Environmental Microbiology, 1999, 65(4): 1746–1752

    CAS  Google Scholar 

  66. Wagner M, Nielsen P H, Loy A, Nielsen J L, Daims H. Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays. Current Opinion in Biotechnology, 2006, 17(1): 83–91

    Article  CAS  Google Scholar 

  67. Nielsen J L, Christensen D, Kloppenborg M, Nielsen P H. Quantification of cell-specific substrate uptake by probe-defined bacteria under in situ conditions by microautoradiography and fluorescence in situ hybridization. Environmental Microbiology, 2003, 5(3): 202–211

    Article  CAS  Google Scholar 

  68. Neufeld J D, Wagner M, Murrell J C. Who eats what, where and when? Isotope-labelling experiments are coming of age. ISME J, 2007, 1(2): 103–110

    Article  CAS  Google Scholar 

  69. Boschker H T S, Nold S C, Wellsbury P, Bos D, de Graaf W, Pel R, Parkes R J, Cappenberg T E. Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature, 1998, 392(6678): 801–805

    Article  CAS  Google Scholar 

  70. Radajewski S, Ineson P, Parekh N R, Murrell J C. Stable-isotope probing as a tool in microbial ecology. Nature, 2000, 403(6770): 646–649

    Article  CAS  Google Scholar 

  71. Manefield M, Whiteley A S, Griffiths R I, Bailey M J. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Applied and Environmental Microbiology, 2002, 68(11): 5367–5373

    Article  CAS  Google Scholar 

  72. Friedrich M W. Stable-isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metagenomes. Current Opinion in Biotechnology, 2006, 17(1): 59–66

    Article  CAS  Google Scholar 

  73. Whiteley A S, Manefield M, Lueders T. Unlocking the ‘microbial black box’ using RNA-based stable isotope probing technologies. Current Opinion in Biotechnology, 2006, 17(1): 67–71

    Article  CAS  Google Scholar 

  74. Schena M, Shalon D, Davis R W, Brown P O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 1995, 270(5235): 467–470

    Article  CAS  Google Scholar 

  75. Roh S W, Abell G C J, Kim K H, Nam Y D, Bae J W. Comparing microarrays and next-generation sequencing technologies for microbial ecology research. Trends in Biotechnology, 2010, 28(6): 291–299

    Article  CAS  Google Scholar 

  76. Gentry T J, Wickham G S, Schadt C W, He Z, Zhou J. Microarray applications in microbial ecology research. Microbial Ecology, 2006, 52(2): 159–175

    Article  CAS  Google Scholar 

  77. Duc L, Neuenschwander S, Rehrauer H, Wagner U, Sobek J, Schlapbach R, Zeyer J. Development and experimental validation of a nifH oligonucleotide microarray to study diazotrophic communities in a glacier forefield. Environmental Microbiology, 2009, 11(8): 2179–2189

    Article  CAS  Google Scholar 

  78. He Z L, Gentry T J, Schadt C W, Wu L Y, Liebich J, Chong S C, Huang Z J, Wu W M, Gu B H, Jardine P, Criddle C, Zhou J. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J, 2007, 1(1): 67–77

    Article  CAS  Google Scholar 

  79. Zhou J H. Microarrays for bacterial detection and microbial community analysis. Current Opinion in Microbiology, 2003, 6(3): 288–294

    Article  CAS  Google Scholar 

  80. Rivas L A, García-Villadangos M, Moreno-Paz M, Cruz-Gil P, Gómez-Elvira J, Parro V. A 200-antibody microarray biochip for environmental monitoring: searching for universal microbial biomarkers through immunoprofiling. Analytical Chemistry, 2008, 80(21): 7970–7979

    Article  CAS  Google Scholar 

  81. Rich V I, Konstantinidis K, DeLong E F. Design and testing of ‘genome-proxy’ microarrays to profile marine microbial communities. Environmental Microbiology, 2008, 10(2): 506–521

    Article  CAS  Google Scholar 

  82. Raes J, Bork P. Molecular eco-systems biology: towards an understanding of community function. Nature Reviews Microbiology, 2008, 6(9): 693–699

    Article  CAS  Google Scholar 

  83. Hultman J, Ritari J, Romantschuk M, Paulin L, Auvinen P. Universal ligation-detection-reaction microarray applied for compost microbes. BMC Microbiology, 2008, 8:237–251.

    Article  CAS  Google Scholar 

  84. Nyberg L, Turco R F, Nies L. Assessing the impact of nanomaterials on anaerobic microbial communities. Environmental Science & Technology, 2008, 42(6): 1938–1943

    Article  CAS  Google Scholar 

  85. Drees K P, Neilson J W, Betancourt J L, Quade J, Henderson D A, Pryor B M, Maier R M. Bacterial community structure in the hyperarid core of the Atacama Desert, Chile. Applied and Environmental Microbiology, 2006, 72(12): 7902–7908

    Article  CAS  Google Scholar 

  86. Duineveld B M, Rosado A S, van Elsas J D, van Veen J A. Analysis of the dynamics of bacterial communities in the rhizosphere of the chrysanthemum via denaturing gradient gel electrophoresis and substrate utilization patterns. Applied and Environmental Microbiology, 1998, 64(12): 4950–4957

    CAS  Google Scholar 

  87. Weidler G W, Gerbl F W, Stan-Lotter H. Crenarchaeota and their role in the nitrogen cycle in a subsurface radioactive thermal spring in the Austrian Central Alps. Applied and Environmental Microbiology, 2008, 74(19): 5934–5942

    Article  CAS  Google Scholar 

  88. Otawa K, Asano R, Ohba Y, Sasaki T, Kawamura E, Koyama F, Nakamura S, Nakai Y. Molecular analysis of ammonia-oxidizing bacteria community in intermittent aeration sequencing batch reactors used for animal wastewater treatment. Environmental Microbiology, 2006, 8(11): 1985–1996

    Article  CAS  Google Scholar 

  89. Chen X P, Zhu Y G, Xia Y, Shen J P, He J Z. Ammonia-oxidizing archaea: important players in paddy rhizosphere soil? Environmental Microbiology, 2008, 10(8): 1978–1987

    Article  CAS  Google Scholar 

  90. Weinert N, Meincke R, Gottwald C, Heuer H, Gomes N C M, Schloter M, Berg G, Smalla K. Rhizosphere communities of genetically modified zeaxanthin-accumulating potato plants and their parent cultivar differ less than those of different potato cultivars. Applied and Environmental Microbiology, 2009, 75(12): 3859–3865

    Article  CAS  Google Scholar 

  91. Kowalchuk G A, Stienstra A W, Heilig G H J, Stephen J R, Woldendorp J W. Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands. Environmental Microbiology, 2000, 2(1): 99–110

    Article  CAS  Google Scholar 

  92. Henckel T, Friedrich M, Conrad R. Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. Applied and Environmental Microbiology, 1999, 65(5): 1980–1990

    CAS  Google Scholar 

  93. Wertz S, Dandie C E, Goyer C, Trevors J T, Patten C L. Diversity of nirK denitrifying genes and transcripts in an agricultural soil. Applied and Environmental Microbiology, 2009, 75(23): 7365–7377

    Article  CAS  Google Scholar 

  94. Glausiusz J. Extreme culture. Nature, 2007, 447(7147): 905–906

    Article  CAS  Google Scholar 

  95. Meroth C B, Hammes WP, Hertel C. Identification and population dynamics of yeasts in sourdough fermentation processes by PCRdenaturing gradient gel electrophoresis. Applied and Environmental Microbiology, 2003, 69(12): 7453–7461

    Article  CAS  Google Scholar 

  96. Crump B C, Koch E W. Attached bacterial populations shared by four species of aquatic angiosperms. Applied and Environmental Microbiology, 2008, 74(19): 5948–5957

    Article  CAS  Google Scholar 

  97. Cébron A, Coci M, Garnier J, Laanbroek H J. Denaturing gradient gel electrophoretic analysis of ammonia-oxidizing bacterial community structure in the lower Seine River: impact of Paris wastewater effluents. Applied and Environmental Microbiology, 2004, 70(11): 6726–6737

    Article  CAS  Google Scholar 

  98. Hallin S, Lydmark P, Kokalj S, Hermansson M, Sörensson F, Jarvis A, Lindgren P E. Community survey of ammonia-oxidizing bacteria in full-scale activated sludge processes with different solids retention time. Journal of Applied Microbiology, 2005, 99(3): 629–640

    Article  CAS  Google Scholar 

  99. Cardenas E, Wu W M, Leigh M B, Carley J, Carroll S, Gentry T, Luo J, Watson D, Gu B, Ginder-Vogel M, Kitanidis P K, Jardine P M, Zhou J, Criddle C S, Marsh T L, Tiedje J M. Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels. Applied and Environmental Microbiology, 2008, 74(12): 3718–3729

    Article  CAS  Google Scholar 

  100. Wu W M, Carley J, Luo J, Ginder-Vogel M A, Cardenas E, Leigh M B, Hwang C, Kelly S D, Ruan C, Wu L, van Nostrand J, Gentry T, Lowe K, Mehlhorn T, Carroll S, Luo W, Fields M W, Gu B, Watson D, Kemner K M, Marsh T, Tiedje J, Zhou J, Fendorf S, Kitanidis P K, Jardine P M, Criddle C S. In situ bioreduction of uranium (VI) to submicromolar levels and reoxidation by dissolved oxygen. Environmental Science & Technology, 2007, 41(16): 5716–5723

    Article  CAS  Google Scholar 

  101. Gao DW, Fu Y, Tao Y, Li X, Xing M, Gao X H, Ren N Q, Linking microbial community structure to membrane biofouling associated with varying dissolved oxygen. Bioresource Technology, 2010 DOI: 10.1016/j.biortech. 2011.02.039

  102. White H K, Reimers C E, Cordes E E, Dilly G F, Girguis P R. Quantitative population dynamics of microbial communities in plankton-fed microbial fuel cells. ISME J, 2009, 3(6): 635–646

    Article  Google Scholar 

  103. Jong B C, Kim B H, Chang I S, Liew PWY, Choo Y F, Kang G S. Enrichment, performance, and microbial diversity of a thermophilic mediatorless microbial fuel cell. Environmental Science & Technology, 2006, 40(20): 6449–6454

    Article  CAS  Google Scholar 

  104. Cytryn E, Minz D, Gelfand I, Neori A, Gieseke A, de Beer D, van Rijn J. Sulfide-oxidizing activity and bacterial community structure in a fluidized bed reactor from a zero-discharge mariculture system. Environmental Science & Technology, 2005, 39(6): 1802–1810

    Article  CAS  Google Scholar 

  105. Martineau C, Whyte L G, Greer C W. Stable isotope probing analysis of the diversity and activity of methanotrophic bacteria in soils from the Canadian high Arctic. Applied and Environmental Microbiology, 2010, 76(17): 5773–5784

    Article  CAS  Google Scholar 

  106. Lukow T 1, Dunfield P F, Liesack W. Use of the T-RFLP technique to assess spatial and temporal changes in the bacterial community structure within an agricultural soil planted with transgenic and non-transgenic potato plants. FEMS Microbiology Ecology, 2000, 32(3): 241–247

    Article  CAS  Google Scholar 

  107. Dunbar J, Ticknor L O, Kuske C R. Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis. Applied and Environmental Microbiology, 2000, 66(7): 2943–2950

    Article  CAS  Google Scholar 

  108. Tom-Petersen A, Leser T D, Marsh T L, Nybroe O. Effects of copper amendment on the bacterial community in agricultural soil analyzed by the T-RFLP technique. FEMS Microbiology Ecology, 2003, 46(1): 53–62

    Article  CAS  Google Scholar 

  109. Morales S E, Mouser P J, Ward N, Hudman S P, Gotelli N J, Ross D S, Lewis T A. Comparison of bacterial communities in New England Sphagnum bogs using terminal restriction fragment length polymorphism (T-RFLP). Microbial Ecology, 2006, 52(1): 34–44

    Article  CAS  Google Scholar 

  110. Lepère C, Boucher D, Jardillier L, Domaizon I, Debroas D. Succession and regulation factors of small eukaryote community composition in a lacustrine ecosystem (Lake Pavin). Applied and Environmental Microbiology, 2006, 72(4): 2971–2981

    Article  CAS  Google Scholar 

  111. Mills H J, Hunter E, Humphrys M, Kerkhof L, McGuinness L, Huettel M, Kostka J E. Characterization of nitrifying, denitrifying, and overall bacterial communities in permeable marine sediments of the northeastern Gulf of Mexico. Applied and Environmental Microbiology, 2008, 74(14): 4440–4453

    Article  CAS  Google Scholar 

  112. Swan B K, Ehrhardt C J, Reifel K M, Moreno L I, Valentine D L. Archaeal and bacterial communities respond differently to environmental gradients in anoxic sediments of a California hypersaline lake, the Salton Sea. Applied and Environmental Microbiology, 2010, 76(3): 757–768

    Article  CAS  Google Scholar 

  113. Whang L M, Chien I C, Yuan S L, Wu Y J. Nitrifying community structures and nitrification performance of full-scale municipal and swine wastewater treatment plants. Chemosphere, 2009, 75(2): 234–242

    Article  CAS  Google Scholar 

  114. Collins G, Woods A, McHugh S, Carton M W, O’Flaherty V. Microbial community structure and methanogenic activity during start-up of psychrophilic anaerobic digesters treating synthetic industrial wastewaters. FEMS Microbiology Ecology, 2003, 46(2): 159–170

    Article  CAS  Google Scholar 

  115. Gao D, Zhang T, Tang C Y, Wu WM, Wong C Y, Lee Y H, Yeh D H, Criddle C S. Membrane fouling in an anaerobic membrane bioreactor: differences in relative abundance of bacterial species in the membrane foulant layer and insuspension. Journal ofMembrane Science, 2010

  116. Pang C M, Liu W T. Community structure analysis of reverse osmosis membrane biofilms and the significance of Rhizobiales bacteria in biofouling. Environmental Science & Technology, 2007, 41(13): 4728–4734

    Article  CAS  Google Scholar 

  117. Saikaly P E, Stroot P G, Oerther D B. Use of 16S rRNA gene terminal restriction fragment analysis to assess the impact of solids retention time on the bacterial diversity of activated sludge. Applied and Environmental Microbiology, 2005, 71(10): 5814–5822

    Article  CAS  Google Scholar 

  118. Madden A S, Smith A C, Balkwill D L, Fagan L A, Phelps T J. Microbial uranium immobilization independent of nitrate reduction. Environmental Microbiology, 2007, 9(9): 2321–2330

    Article  CAS  Google Scholar 

  119. Kennedy N, Edwards S, Clipson N. Soil bacterial and fungal community structure across a range of unimproved and semi-improved upland grasslands. Microbial Ecology, 2005, 50(3): 463–473

    Article  Google Scholar 

  120. Hidri Y, Bouziri L, Maron P A, Anane M, Jedidi N, Hassan A, Ranjard L. Soil DNA evidence for altered microbial diversity after long-term application of municipal wastewater. Agronomy for Sustainable Development, 2010, 30(2): 423–431

    Article  CAS  Google Scholar 

  121. Kent A D, Jones S E, Yannarell A C, Graham J M, Lauster G H, Kratz T K, Triplett E W. Annual patterns in bacterioplankton community variability in a humic lake. Microbial Ecology, 2004, 48(4): 550–560

    Article  CAS  Google Scholar 

  122. Graham J M, Kent A D, Lauster G H, Yannarell A C, Graham L E, Triplett E W. Seasonal dynamics of phytoplankton and planktonic protozoan communities in a northern temperate humic lake: diversity in a dinoflagellate dominated system. Microbial Ecology, 2004, 48(4): 528–540

    Article  CAS  Google Scholar 

  123. Wood S A, Jentzsch K, Rueckert A, Hamilton D P, Cary S C. Hindcasting cyanobacterial communities in Lake Okaro with germination experiments and genetic analyses. FEMS Microbiology Ecology, 2009, 67(2): 252–260

    Article  CAS  Google Scholar 

  124. Nold S C, Pangborn J B, Zajack H A, Kendall S T, Rediske R R, Biddanda B A. Benthic bacterial diversity in submerged sinkhole ecosystems. Applied and Environmental Microbiology, 2010, 76(1): 347–351

    Article  CAS  Google Scholar 

  125. Borin S, Marzorati M, Cavalca L, Sorlini C, Daffonchio D, Zilli M, Converti A, Cherif H, Hassen A. Diversity of the microflora of a compost-packed biofilter treating benzene-contaminated air. European Symposium on Environmental Biotechnology, Eseb 2004, 2004: 75–79

    Google Scholar 

  126. Steele J A, Ozis F, Fuhrman J A, Devinny J S. Structure of microbial communities in ethanol biofilters. Chemical Engineering Journal, 2005, 113(2–3): 135–143

    Article  CAS  Google Scholar 

  127. Vanysacker L, Declerck S A J, Hellemans B, de Meester L, Vankelecom I, Declerck P. Bacterial community analysis of activated sludge: an evaluation of four commonly used DNA extraction methods. Applied Microbiology and Biotechnology, 2010, 88(1): 299–307

    Article  CAS  Google Scholar 

  128. Zhang X, Brussee K, Coutinho C T, Rooney-Varga J N. Chemical stress induced by copper: examination of a biofilm system. Water Science and Technology, 2006, 54(9): 191–199

    Article  CAS  Google Scholar 

  129. Hewson I, Fuhrman J A. Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia. Applied and Environmental Microbiology, 2004, 70(6): 3425–3433

    Article  CAS  Google Scholar 

  130. Popa R, Popa R, Mashall M J, Nguyen H, Tebo B M, Brauer S. Limitations and benefits of ARISA intra-genomic diversity fingerprinting. Journal of Microbiological Methods, 2009, 78(2): 111–118

    Article  CAS  Google Scholar 

  131. Kovacs A, Yacoby K, Gophna U. A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness. Research in Microbiology, 2010, 161(3): 192–197

    Article  CAS  Google Scholar 

  132. de Vero L, Gala E, Gullo M, Solieri L, Landi S, Giudici P. Application of denaturing gradient gel electrophoresis (DGGE) analysis to evaluate acetic acid bacteria in traditional balsamic vinegar. Food Microbiology, 2006, 23(8): 809–813

    Article  CAS  Google Scholar 

  133. Meays C L, Broersma K, Nordin R, Mazumder A. Source tracking fecal bacteria in water: a critical review of current methods. Journal of Environmental Management, 2004, 73(1): 71–79

    Article  Google Scholar 

  134. Middleton S A, Anzenberger G, Knapp L A. Denaturing gradient gel electrophoresis (DGGE) screening of clones prior to sequencing. Molecular Ecology Notes, 2004, 4(4): 776–778

    Article  CAS  Google Scholar 

  135. Talbot G, Topp E, Palin M F, Massé D I. Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors. Water Research, 2008, 42(3): 513–537

    Article  CAS  Google Scholar 

  136. Gilbride K A, Lee D Y, Beaudette L A. Molecular techniques in wastewater: understanding microbial communities, detecting pathogens, and real-time process control. Journal of Microbiological Methods, 2006, 66(1): 1–20

    Article  CAS  Google Scholar 

  137. Bernhard A E, Colbert D, McManus J, Field K G. Microbial community dynamics based on 16S rRNA gene profiles in a Pacific Northwest estuary and its tributaries. FEMS Microbiology Ecology, 2005, 52(1): 115–128

    Article  CAS  Google Scholar 

  138. Kan J, Suzuki M T, Wang K, Evans S E, Chen F. High temporal but low spatial heterogeneity of bacterioplankton in the Chesapeake Bay. Applied and Environmental Microbiology, 2007, 73(21): 6776–6789

    Article  CAS  Google Scholar 

  139. Cardinale M, Brusetti L, Quatrini P, Borin S, Puglia A M, Rizzi A, Zanardini E, Sorlini C, Corselli C, Daffonchio D. Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. Applied and Environmental Microbiology, 2004, 70(10): 6147–6156

    Article  CAS  Google Scholar 

  140. Tiirola M, Lahtinen T, Vuento M, Oker-Blom C. Early succession of bacterial biofilms in paper machines. Journal of Industrial Microbiology & Biotechnology, 2009, 36(7): 929–937

    Article  CAS  Google Scholar 

  141. Okubo A, Sugiyama S. Comparison of molecular fingerprinting methods for analysis of soil microbial community structure. Ecological Research, 2009, 24(6): 1399–1405

    Article  Google Scholar 

  142. Danovaro R, Luna G M, Dell’anno A, Pietrangeli B. Comparison of two fingerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of bacterial diversity in aquatic environments. Applied and Environmental Microbiology, 2006, 72(9): 5982–5989

    Article  CAS  Google Scholar 

  143. Ramette A. Quantitative community fingerprinting methods for estimating the abundance of operational taxonomic units in natural microbial communities. Applied and Environmental Microbiology, 2009, 75(8): 2495–2505

    Article  CAS  Google Scholar 

  144. Yannarell A C, Triplett E W. Within- and between-lake variability in the composition of bacterioplankton communities: investigations using multiple spatial scales. Applied and Environmental Microbiology, 2004, 70(1): 214–223

    Article  CAS  Google Scholar 

  145. Wilderer P A, Bungartz H J, Lemmer H, Wagner M, Keller J, Wuertz S. Modern scientific methods and their potential in wastewater science and technology. Water Research, 2002, 36(2): 370–393

    Article  CAS  Google Scholar 

  146. Sekar R, Pernthaler A, Pernthaler J, Warnecke F, Posch T, Amann R. An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization. Applied and Environmental Microbiology, 2003, 69(5): 2928–2935

    Article  CAS  Google Scholar 

  147. Miura Y, Okabe S. Quantification of cell specific uptake activity of microbial products by uncultured Chloroflexi by microautoradiography combined with fluorescence in situ hybridization. Environmental Science & Technology, 2008, 42(19): 7380–7386

    Article  CAS  Google Scholar 

  148. Nielsen J L, Christensen D, Kloppenborg M, Nielsen P H. Quantification of cell-specific substrate uptake by probe-defined bacteria under in situ conditions by microautoradiography and fluorescence in situ hybridization. Environmental Microbiology, 2003, 5(3): 202–211

    Article  CAS  Google Scholar 

  149. Nielsen J L, Nielsen P H. Advances in microscopy: microautor-adiography of single cells. Methods in Enzymology, 2005, 397: 237–256

    Article  CAS  Google Scholar 

  150. Yin H Q, Cao L H, Qiu G Z, Wang D Z, Kellogg L, Zhou J Z, Dai Z M, Liu X D. Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in Acid Mine Drainages and bioleaching systems. Journal of Microbiological Methods, 2007, 70(1): 165–178

    Article  CAS  Google Scholar 

  151. Wilson K H, Wilson W J, Radosevich J L, DeSantis T Z, Viswanathan V S, Kuczmarski T A, Andersen G L. High-density microarray of small-subunit ribosomal DNA probes. Applied and Environmental Microbiology, 2002, 68(5): 2535–2541

    Article  CAS  Google Scholar 

  152. Wu L Y, Thompson D K, Liu X D, Fields M W, Bagwell C E, Tiedje J M, Zhou J Z. Development and evaluation of microarraybased whole-genome hybridization for detection of microorganisms within the context of environmental applications. Environmental Science & Technology, 2004, 38(24): 6775–6782

    Article  CAS  Google Scholar 

  153. Wu L Y, Thompson D K, Li G S, Hurt R A, Tiedje J M, Zhou J Z. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Applied and Environmental Microbiology, 2001, 67(12): 5780–5790

    Article  CAS  Google Scholar 

  154. Shalon D, Smith S J, Brown P O. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Research, 1996, 6(7): 639–645

    Article  CAS  Google Scholar 

  155. Bent S J, Forney L J. The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. ISME J, 2008, 2(7): 689–695

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Dawen Gao.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gao, D., Tao, Y. Current molecular biologic techniques for characterizing environmental microbial community. Front. Environ. Sci. Eng. 6, 82–97 (2012). https://doi.org/10.1007/s11783-011-0306-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11783-011-0306-6

Keywords

Navigation