Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities

Frontiers of Environmental Science and Engineering in China

Volumn 5, Issue 1, 2011, Pages 1-20

  He, Zhili ^a   Van Nostrand, Joy D ^a   Deng, Ye ^a   Zhou, Jizhong ^a,b,c  

^a UNIVERSITY OF OKLAHOMA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c TSINGHUA UNIVERSITY   (China)

Author keywords

ecosystem functioning; environmental factor; functional diversity composition structure; functional gene arrays (FGAs); GeoChip; microbial communities

Indexed keywords

EID: 78650946023     PISSN: 16737415     EISSN: 16737520     Source Type: Journal    
DOI: 10.1007/s11783-011-0301-y     Document Type: Article

References (111)

1. Torsvik V, Øvreås L, Thingstad T F. Prokaryotic diversity-magnitude, dynamics, and controlling factors. Science, 2002, 296(5570): 1064-1066.
2. Roesch L F, Fulthorpe R R, Riva A, Casella G, Hadwin A K, Kent A D, Daroub S H, Camargo F A, Farmerie W G, Triplett E W. Pyrosequencing enumerates and contrasts soil microbial diversity. The ISME Journal, 2007, 1(4): 283-290.
3. Schloss P D, Handelsman J. Toward a census of bacteria in soil. PLoS Computational Biology, 2006, 2(7): e92.
4. Hong S H, Bunge J, Jeon S O, Epstein S S. Predicting microbial species richness. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(1): 117-122.
5. Curtis T P, Sloan W T, Scannell J W. Estimating prokaryotic diversity and its limits. Proceedings of the National Academy of Sciences of the United States of America, 2002, 99(16): 10494-10499.
6. Gans J, Wolinsky M, Dunbar J. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science, 2005, 309(5739): 1387-1390.
7. Whitman WB, Coleman D C, Wiebe W J. Prokaryotes: the unseen majority. Proceedings of the National Academy of Sciences of the United States of America, 1998, 95(12): 6578-6583.
8. Dunbar J, Barns S M, Ticknor L O, Kuske C R. Empirical and theoretical bacterial diversity in four Arizona soils. Applied and Environmental Microbiology, 2002, 68(6): 3035-3045.
9. Steward G F, Jenkins B D, Ward B B, Zehr J P. Development and testing of a DNA macroarray to assess nitrogenase (nifH) gene diversity. Applied and Environmental Microbiology, 2004, 70(3): 1455-1465.
10. Jenkins B D, Steward G F, Short S M, Ward B B, Zehr J P. Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarray. Applied and Environmental Microbiology, 2004, 70(3): 1767-1776.
11. Warnecke P M, Stirzaker C, Melki J R, Millar D S, Paul C L, Clark S J. Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA. Nucleic Acids Research, 1997, 25(21): 4422-4426.
12. Lueders T, Friedrich M W. Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Applied and Environmental Microbiology, 2003, 69(1): 320-326.
13. Suzuki M T, Giovannoni S J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Applied and Environmental Microbiology, 1996, 62(2): 625-630.
14. 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.
15. Guschin D Y, Mobarry B K, Proudnikov D, Stahl D A, Rittmann B E, Mirzabekov A D. Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Applied and Environmental Microbiology, 1997, 63(6): 2397-2402.
16. Zhou J, Kang S, Schadt C W, Garten C T Jr. Spatial scaling of functional gene diversity across various microbial taxa. Proceedings of the National Academy of Sciences of the United States of America, 2008, 105(22): 7768-7773.
17. He Z, Deng Y, van Nostrand J D, Tu Q, Xu M, Hemme C L, Li X, Wu L, Gentry T J, Yin Y, Liebich J, Hazen T C, Zhou J. GeoChip 3. 0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. The ISME Journal, 2010, 4(9): 1167-1179.
18. Wu L, Thompson D K, Li G, Hurt R A, Tiedje J M, Zhou J. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Applied and Environmental Microbiology, 2001, 67(12): 5780-5790.
19. Rhee S K, Liu X, Wu L, Chong S C, Wan X, Zhou J. Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Applied and Environmental Microbiology, 2004, 70(7): 4303-4317.
20. 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.
21. He Z, Gentry T J, Schadt CW, Wu L, Liebich J, Chong S C, Huang Z, Wu W, Gu B, Jardine P, Criddle C, Zhou J. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. The ISME Journal, 2007, 1(1): 67-77.
22. Taroncher-Oldenburg G, Griner E M, Francis C A, Ward B B. Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Applied and Environmental Microbiology, 2003, 69(2): 1159-1171.
23. Zhang L, Hurek T, Reinhold-Hurek B. A nifH-based oligonucleotide microarray for functional diagnostics of nitrogen-fixing microorganisms. Microbial Ecology, 2007, 53(3): 456-470.
24. Bontemps C, Golfier G, Gris-Liebe C, Carrere S, Talini L, Boivin-Masson C. Microarray-based detection and typing of the Rhizobium nodulation gene nodC: potential of DNA arrays to diagnose biological functions of interest. Applied and Environmental Microbiology, 2005, 71(12): 8042-8048.
25. Bodrossy L, Stralis-Pavese N, Murrell J C, Radajewski S, Weilharter A, Sessitsch A. Development and validation of a diagnostic microbial microarray for methanotrophs. Environmental Microbiology, 2003, 5(7): 566-582.
26. Stralis-Pavese N, Sessitsch A, Weilharter A, Reichenauer T, Riesing J, Csontos J, Murrell J C, Bodrossy L. Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environmental Microbiology, 2004, 6(4): 347-363.
27. Bodrossy L, Stralis-Pavese N, Konrad-Köszler M, Weilharter A, Reichenauer T G, Schöfer D, Sessitsch A. mRNA-based parallel detection of active methanotroph populations by use of a diagnostic microarray. Applied and Environmental Microbiology, 2006, 72(2): 1672-1676.
28. Miller S M, Tourlousse D M, Stedtfeld R D, Baushke SW, Herzog A B, Wick L M, Rouillard J M, Gulari E, Tiedje J M, Hashsham S A. In situ-synthesized virulence and marker gene biochip for detection of bacterial pathogens in water. Applied and Environmental Microbiology, 2008, 74(7): 2200-2209.
29. Call D R, Bakko M K, Krug M J, Roberts M C. Identifying antimicrobial resistance genes with DNA microarrays. Antimicrobial Agents and Chemotherapy, 2003, 47(10): 3290-3295.
30. Kostić T, Weilharter A, Sessitsch A, Bodrossy L. High-sensitivity, polymerase chain reaction-free detection of microorganisms and their functional genes using 70-mer oligonucleotide diagnostic microarray. Analytical Biochemistry, 2005, 346(2): 333-335.
31. Cleven B E E, Palka-Santini M, Gielen J, Meembor S, Krönke M, Krut O. Identification and characterization of bacterial pathogens causing bloodstream infections by DNA microarray. Journal of Clinical Microbiology, 2006, 44(7): 2389-2397.
32. Palka-Santini M, Cleven B E, Eichinger L, Krönke M, Krut O. Large scale multiplex PCR improves pathogen detection by DNA microarrays. BMC Microbiology, 2009, 9(1): 1.
33. Yin H, Cao L, Qiu G, Wang D, Kellogg L, Zhou J, Dai Z, Liu X. 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.
34. Tiquia S M, Wu L, Chong S C, Passovets S, Xu D, Xu Y, Zhou J. Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. BioTechniques, 2004, 36(4): 664-670, 672, 674-675.
35. Liang Y, He Z, Wu L, Deng Y, Li G, Zhou J. Development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities. Applied and Environmental Microbiology, 2010, 76(4): 1088-1094.
36. Zhou J, He Z, van Nostrand J D, Wu L, Deng Y. Applying GeoChip analysis to disparate microbial communities. Microbe, 2010, 5: 60-65.
37. Wilson K H, Blitchington R B, Greene R C. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. Journal of Clinical Microbiology, 1990, 28(9): 1942-1946.
38. Amann R I, Ludwig W, Schleifer K H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews, 1995, 59(1): 143-169.
39. Yamamoto S, Harayama S. PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Applied and Environmental Microbiology, 1995, 61(3): 1104-1109.
40. Hugenholtz P, Goebel B M, Pace N R. Impact of cultureindependent studies on the emerging phylogenetic view of bacterial diversity. Journal of Bacteriology, 1998, 180(18): 4765-4774.
41. Brodie E L, Desantis T Z, Joyner D C, Baek S M, Larsen J T, Andersen G L, Hazen T C, Richardson P M, Herman D J, Tokunaga T K, Wan J M, Firestone M K. Application of a highdensity oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Applied and Environmental Microbiology, 2006, 72(9): 6288-6298.
42. Liesegang H, Lemke K, Siddiqui R A, Schlegel H G. Characterization of the inducible nickel and cobalt resistance determinant cnr from pMOL28 of Alcaligenes eutrophus CH34. Journal of Bacteriology, 1993, 175(3): 767-778.
43. Grass G, Grosse C, Nies D H. Regulation of the cnr cobalt and nickel resistance determinant from Ralstonia sp. strain CH34. Journal of Bacteriology, 2000, 182(5): 1390-1398.
44. Tibazarwa C, Wuertz S, Mergeay M, Wyns L, van Der Lelie D. Regulation of the cnr cobalt and nickel resistance determinant of Ralstonia eutropha (Alcaligenes eutrophus) CH34. Journal of Bacteriology, 2000, 182(5): 1399-1409.
45. Nies D H. Efflux-mediated heavy metal resistance in prokaryotes. FEMS Microbiology Reviews, 2003, 27(2-3): 313-339.
46. Saier M H Jr, Tam R, Reizer A, Reizer J. Two novel families of bacterial membrane proteins concerned with nodulation, cell division and transport. Molecular Microbiology, 1994, 11(5): 841-847.
47. Paulsen I T, Park J H, Choi P S, Saier M H Jr. A family of gramnegative bacterial outer membrane factors that function in the export of proteins, carbohydrates, drugs and heavy metals from gram-negative bacteria. FEMS Microbiology Letters, 1997, 156(1): 1-8.
48. Eddy S R. Profile hidden Markov models. Bioinformatics (Oxford, England), 1998, 14(9): 755-763.
49. Thompson J D, Higgins D G, Gibson T J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 1994, 22(22): 4673-4680.
50. Li X, He Z, Zhou J. Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Research, 2005, 33(19): 6114-6123.
51. Liebich J, Schadt C W, Chong S C, He Z, Rhee S K, Zhou J. Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications. Applied and Environmental Microbiology, 2006, 72(2): 1688-1691.
52. He Z, Wu L, Li X, Fields MW, Zhou J. Empirical establishment of oligonucleotide probe design criteria. Applied and Environmental Microbiology, 2005, 71(7): 3753-3760.
53. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. Journal of Computational Biology, 2000, 7(1-2): 203-214.
54. Zhou J, Bruns M A, Tiedje J M. DNA recovery from soils of diverse composition. Applied and Environmental Microbiology, 1996, 62(2): 316-322.
55. Hurt R A, Qiu X, Wu L, Roh Y, Palumbo A V, Tiedje J M, Zhou J. Simultaneous recovery of RNA and DNA from soils and sediments. Applied and Environmental Microbiology, 2001, 67(10): 4495-4503.
56. Liang Y, Li G, van Nostrand J D, He Z, Wu L, Deng Y, Zhang X, Zhou J. Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field. FEMS Microbiology Ecology, 2009, 70(2): 324-333.
57. Ning J, Liebich J, Kästner M, Zhou J, Schäffer A, Burauel P. Different influences of DNA purity indices and quantity on PCRbased DGGE and functional gene microarray in soil microbial community study. Applied Microbiology and Biotechnology, 2009, 82(5): 983-993.
58. Wu L, Liu X, Schadt C W, Zhou J. Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Applied and Environmental Microbiology, 2006, 72(7): 4931-4941.
59. Bürgmann H, Widmer F, Sigler W V, Zeyer J. mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Applied and Environmental Microbiology, 2003, 69(4): 1928-1935.
60. McGrath K C, Thomas-Hall S R, Cheng C T, Leo L, Alexa A, Schmidt S, Schenk P M. Isolation and analysis of mRNA from environmental microbial communities. Journal of Microbiological Methods, 2008, 75(2): 172-176.
61. Gao H, Yang Z K, Gentry T J, Wu L, Schadt C W, Zhou J. Microarray-based analysis of microbial community RNAs by whole-community RNA amplification. Applied and Environmental Microbiology, 2007, 73(2): 563-571.
62. He Z, Wu L, Fields M W, Zhou J. Use of microarrays with different probe sizes for monitoring gene expression. Applied and Environmental Microbiology, 2005, 71(9): 5154-5162.
63. van Nostrand J D, Wu W M, Wu L, Deng Y, Carley J, Carroll S, He Z, Gu B, Luo J, Criddle C S, Watson D B, Jardine PM, Marsh T L, Tiedje J M, Hazen T C, Zhou J. GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer. Environmental Microbiology, 2009, 11(10): 2611-2626.
64. Waldron P J, Wu L, van Nostrand J D, Schadt C W, He Z, Watson D B, Jardine P M, Palumbo A V, Hazen T C, Zhou J. Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels. Environmental Science & Technology, 2009, 43(10): 3529-3534.
65. Mason O U, Di Meo-Savoie C A, van Nostrand J D, Zhou J, Fisk M R, Giovannoni S J. Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts. The ISME Journal, 2009, 3(2): 231-242.
66. He Z, Zhou J. Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis. Applied and Environmental Microbiology, 2008, 74(10): 2957-2966.
67. He Z, van Nostrand J D, Wu L, Zhou J. Development and application of functional gene arrays for microbial community analysis. Transactions of Nonferrous Metals Society of China, 2008, 18(6): 1319-1327.
68. 2 stimulates net accumulations of carbon and nitrogen in land ecosystems: a meta-analysis. Ecology, 2006, 87(1): 53-63.
69. 2. Ecology Letters, 2010, 13(5): 564-575.
70. ter Braak C J F. Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis. Ecology, 1986, 67(5): 1167-1179.
71. Økland R H, Eilertsen O. Canonical correspondence analysis with variation partitioning: some comments and an application. Journal of Vegetation Science, 1994, 5(1): 117-126.
72. Ramette A, Tiedje J M. Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem. Proceedings of the National Academy of Sciences of the United States of America, 2007, 104(8): 2761-2766.
73. Yergeau E, Kang S, He Z, Zhou J, Kowalchuk G A. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. The ISME Journal, 2007, 1(2): 163-179.
74. Wu L, Kellogg L, Devol A H, Tiedje J M, Zhou J. Microarraybased characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico. Applied and Environmental Microbiology, 2008, 74(14): 4516-4529.
75. Wang F, Zhou H, Meng J, Peng X, Jiang L, Sun P, Zhang C, van Nostrand J D, Deng Y, He Z, Wu L, Zhou J, Xiao X. GeoChipbased analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proceedings of the National Academy of Sciences of the United States of America, 2009, 106(12): 4840-4845.
76. Xiong J, Wu L, Tu S, van Nostrand J D, He Z, Zhou J, Wang G. Microbial communities and functional genes associated with soil arsenic contamination and rhizosphere of the arsenic hyperaccumulating plant Pteris vittata L. Applied and Environmental Microbiology, 2010 (in press, AEM. 00500-10).
77. Liu W, Wang A, Cheng S, Logan B E, Yu H, Deng Y, Nostrand J D V, Wu L, He Z, Zhou J. Geochip-based functional gene analysis of anodophilic communities in microbial electrolysis cells under different operational modes. Environmental Science & Technology, 2010, 44(19): 7729-7735.
78. Dennis P, Edwards E A, Liss S N, Fulthorpe R. Monitoring gene expression in mixed microbial communities by using DNA microarrays. Applied and Environmental Microbiology, 2003, 69(2): 769-778.
79. Deng Y, He Z, van Nostrand J D, Zhou J. Design and analysis of mismatch probes for long oligonucleotide microarrays. BMC Genomics, 2008, 9(1): 491.
80. Chen Q, Yin H, Luo H, Xie M, Qiu G, Liu X. Micro-array based whole-genome hybridization for detection of microorganisms in acid mine drainage and bioleaching systems. Hydrometallurgy, 2009, 95(1-2): 96-103.
81. Denef V J, Park J, Rodrigues J L M, Tsoi T V, Hashsham S A, Tiedje JM. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environmental Microbiology, 2003, 5(10): 933-943.
82. Relógio A, Schwager C, Richter A, Ansorge W, Valcárcel J. Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Research, 2002, 30(11): e51.
83. Cho J C, Tiedje J M. Quantitative detection of microbial genes by using DNA microarrays. Applied and Environmental Microbiology, 2002, 68(3): 1425-1430.
84. Zhou J, Thompson D K. Challenges in applying microarrays to environmental studies. Current Opinion in Biotechnology, 2002, 13(3): 204-207.
85. Schaupp C J, Jiang G, Myers T G, Wilson M A. Active mixing during hybridization improves the accuracy and reproducibility of microarray results. BioTechniques, 2005, 38(1): 117-119.
86. Zhou X C, Wu L Y, Zhou J Z. Fabrication of DNA microarrays on nanoengineered polymeric ultrathin film prepared by self-assembly of polyelectrolyte multilayers. Langmuir, 2004, 20(20): 8877-8885.
87. Branham WS, Melvin C D, Han T, Desai V G, Moland C L, Scully A T, Fuscoe J C. Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements. BMC Biotechnology, 2007, 7(1): 8.
88. Kumar A, Larsson O, Parodi D, Liang Z. Silanized nucleic acids: a general platform for DNA immobilization. Nucleic Acids Research, 2000, 28(14): e71.
89. Gudnason H, Dufva M, Duong Bang D, Wolff A. An inexpensive and simple method for thermally stable immobilization of DNA on an unmodified glass surface: UV linking of poly(T)10-poly(C)10-tagged DNA probes. BioTechniques, 2008, 45(3): 261-271.
90. DeSantis T Z, Brodie E L, Moberg J P, Zubieta I X, Piceno Y M, Andersen G L. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microbial Ecology, 2007, 53(3): 371-383.
91. Leigh M B, Pellizari V H, UhlÍk O, Sutka R, Rodrigues J, Ostrom N E, Zhou J, Tiedje J M. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). The ISME Journal, 2007, 1(2): 134-148.
92. Gu B, Brooks S C, Roh Y, Jardine PM. Geochemical reactions and dynamics during titration of a contaminated groundwater with high uranium, aluminum, and calcium. Geochimica et Cosmochimica Acta, 2003, 67(15): 2749-2761.
93. Wu W M, Carley J, Gentry T, Ginder-Vogel M A, Fienen M, Mehlhorn T, Yan H, Caroll S, Pace M N, Nyman J, Luo J, Gentile ME, Fields MW, Hickey R F, Gu B, Watson D, Cirpka O A, Zhou J, Fendorf S, Kitanidis P K, Jardine PM, Criddle C S. Pilot-scale in situ bioremedation of uranium in a highly contaminated aquifer. 2. Reduction of u(VI) and geochemical control of u(VI) bioavailability. Environmental Science & Technology, 2006, 40(12): 3986-3995.
94. 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 D, Gentry T, Lowe K, Mehlhorn T, Carroll S, Luo W, Fields MW, 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.
95. Xu M, Wu W M, Wu L, He Z, van Nostrand J D, Deng Y, Luo J, Carley J, Ginder-Vogel M, Gentry T J, Gu B, Watson D, Jardine P M, Marsh T L, Tiedje J M, Hazen T, Criddle C S, Zhou J. Responses of microbial community functional structures to pilotscale uranium in situ bioremediation. The ISME Journal, 2010, 4(8): 1060-1070.
96. Tas N, van Eekert M H, Schraa G, Zhou J, de Vos W M, Smidt H. Tracking functional guilds: "Dehalococcoides" spp. in European river basins contaminated with hexachlorobenzene. Applied and Environmental Microbiology, 2009, 75(14): 4696-4704.
97. Kimes N E, van Nostrand J D, Weil E, Zhou J, Morris P J. Microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased colonies. Environmental Microbiology, 2010, 12(2): 541-556.
98. Zhang Y, Zhang X, Liu X, Xiao Y, Qu L, Wu L, Zhou J. Microarray-based analysis of changes in diversity of microbial genes involved in organic carbon decomposition following land use/cover changes. FEMS Microbiology Letters, 2007, 266(2): 144-151.
99. Lawton J H. Are there general laws in ecology? Oikos, 1999, 84(2): 177-192.
100. Reich P B, Knops J, Tilman D, Craine J, Ellsworth D, Tjoelker M, Lee T, Wedin D, Naeem S, Bahauddin D, Hendrey G, Jose S, Wrage K, Goth J, Bengston W. Plant diversity enhances ecosystem responses to elevated CO2 and nitrogen deposition. Nature, 2001, 410(6830): 809-812.
101. Parnell J J, Rompato G, Latta L C I V 4th, Pfrender M E, van Nostrand J D, He Z, Zhou J, Andersen G, Champine P, Ganesan B, Weimer B C, Aziz R K. Functional biogeography as evidence of gene transfer in hypersaline microbial communities. PLoS ONE, 2010, 5(9): e12919.
102. Xie J, He Z, Liu X, Liu X, van Nostrand J D, Deng Y, Wu L, Qiu G, Zhou J. Geochip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage. Applied and Environmental Microbiology, 2010.
103. Rodríguez-Martínez EM, Pérez E X, Schadt CW, Zhou J, Massol-Deyá A A. Microbial diversity and bioremediation of a hydrocarbon-contaminated aquifer (Vega Baja, Puerto Rico). International Journal of Environmental Research and Public Health, 2006, 3(3): 292-300.
104. Liang Y, Nostrand J D V, Wang J, Zhang X, Zhou J, Li G. Microarray-based functional gene analysis of soil microbial communities during ozonation and biodegradation of crude oil. Chemosphere, 2009, 75(2): 193-199.
105. Liang Y, van Nostrand J D, Deng Y, He Z, Wu L, Zhang X, Li G, Zhou J. Functional gene diversity of soil microbial communities from five oil-contaminated fields in China. The ISME Journal, 2010, (in press).
106. Hazen T C, Dubinsky E A, DeSantis T Z, Andersen G L, Piceno Y M, Singh N, Jansson J K, Probst A, Borglin S E, Fortney J L, Stringfellow W T, Bill M, Conrad M E, Tom L M, Chavarria K L, Alusi T R, Lamendella R, Joyner D C, Spier C, Baelum J, Auer M, Zemla M L, Chakraborty R, Sonnenthal E L, D'haeseleer P, Holman H Y N, Osman S, Lu Z, van Nostrand J D, Deng Y, Zhou J, Mason O U. Deep-sea oil plume enriches indigenous oildegrading bacteria. Science, 2010, 330(6001): 204-208.
107. Margulies M, Egholm M, Altman W E, Attiya S, Bader J S, Bemben L A, Berka J, Braverman M S, Chen Y J, Chen Z T, Dewell S B, Du L, Fierro J M, Gomes X V, Godwin B C, He W, Helgesen S, Ho C H, Irzyk G P, Jando S C, Alenquer ML, Jarvie T P, Jirage K B, Kim J B, Knight J R, Lanza J R, Leamon J H, Lefkowitz S M, Lei M, Li J, Lohman K L, Lu H, Makhijani V B, McDade K E, McKenna M P, Myers E W, Nickerson E, Nobile J R, Plant R, Puc B P, Ronan MT, Roth G T, Sarkis G J, Simons J F, Simpson J W, Srinivasan M, Tartaro K R, Tomasz A, Vogt K A, Volkmer G A, Wang S H, Wang Y, Weiner M P, Yu P, Begley R F, Rothberg J M. Genome sequencing in microfabricated highdensity picolitre reactors. Nature, 2005, 437(7057): 376-380.
108. Binladen J, Gilbert M T P, Bollback J P, Panitz F, Bendixen C, Nielsen R, Willerslev E, Hahn M. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE, 2007, 2(2): e197.
109. Hamady M, Walker J J, Harris J K, Gold N J, Knight R. Errorcorrecting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nature Methods, 2008, 5(3): 235-237.
110. Iwai S, Chai B, Sul W J, Cole J R, Hashsham S A, Tiedje J M. Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. The ISME Journal, 2010, 4(2): 279-285.
111. Qin J, Li R, Raes J, Arumugam M, Burgdorf K S, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende D R, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto J M, Hansen T, Le Paslier D, Linneberg A, Nielsen H B, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich S D, Wang J. A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 2010, 464(7285): 59-65.