Microarray Technology and Its Applicability in Soil Science – A Short Review

Stella Asuming- Brempong

Department of Soil Science, School of Agriculture, University of Ghana, Legon, Ghana.

DOI: 10.4236/ojss.2012.23039                

Abstract

The GeoChip is a glass slide containing oligonucleotide probes targeting genes that confer specific function to micro-organism. The GeoChip has been used to dissect the microbial community functional structure of environmental samples. The PhyloChip is a glass slide containing oligonucleotide probes of the 16S rRNA genes and it offers tremendous potential to monitor microbial population. Below ground microbial community can be linked to the above ground plant community by the use of these Chips in a high throughput manner. This review seeks to determine the various roles of the GeoChip and the PhyloChip in soil microbial ecology studies. During biostimulation of uranium in groundwater, microbial community dynamics was linked to functional processes and in global warming studies, microbial response to functional gene structure has been possible by the use of the GeoChip. The PhyloChip, on the other hand, provides more comprehensive survey of the microbial diversity, composition and structure and are less susceptible to the influence of dominance in microbial community. Some of the concerns regarding the use of compost in agricultural soils i.e. the spread of human, animal and plant pathogens were reduced when the PhyloChip was used to monitor composting.

Keywords

GeoChip; PhyloChip; Biodiversity; Microarray

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	A. H. Fitter, G. A. Gilligan, K. Hollingworth, A. Kleczkowski, R. M. Twyman and J. W. Pitchford, “Biodiversity and Ecosystem Function and Soil,” Functional Ecology, Vol. 19, No. 3, 2005, pp. 369-377. doi:10.1111/j.0269-8463.2005.00969.x
[2]	D. Shalon, S. J. Smith and P. O. Brown, “A DNA Microarray System for Analyzing Complex DNA Samples Using Two-Color Fluorescent Probe Hybridization,” Genome Research, Vol. 6, No. 7, 1996, pp. 639-645. doi:10.1101/gr.6.7.639
[3]	J. J. Kelly, “Molecular Techniques for the Analysis of Soil Microbial Processes: Functional Gene Analysis and the Utility of DNA Microarrays,” Soil Science, Vol. 168, No. 9, 2003, pp. 369-377. doi:10.1097/01.ss.0000090800.06903.2e
[4]	Z. He, T. J. Gentry, C. W. Scheldt, L. Wu, J. Liebich, S. C. Cheng, Z. Huang, W. Wu, B. Gu, P. Jardie, C. Criddle and J. Zhou, “GeoChip, a Comprehensive Microarray for Investigating Biogeochemical, Ecological and Environemtal Processes,” ISME Journal, Vol. 1, No. 1, 2007, pp. 67-77. doi:10.1038/ismej.2007.2
[5]	L. Wu, X. Liu, C. W. Schadt and J. Zhou, “Microarray Based Analysis of Subnanogram Quantitites of Microbial Community DNA by Using Whole-Community Genome Amplification,” Applied and Environmental Microbiology, Vol. 72, No. 7, 2006, pp. 4931-4941. doi:10.1128/AEM.02738-05
[6]	L. Wu, D. K. Thompson, G. Li, R. A. Hurt, J. M. Tiedje and J. Zhou, “Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment,” Applied and Environmental Microbiology, Vol. 67, No. 12, 2001, pp. 5780-5790. doi:10.1128/AEM.67.12.5780-5790.2001
[7]	Z. He, Y. Deng, D. J. Van Nostrand, Q. Tu, M. Xuy, C. L. Hemme, X. Li, L. Wu, T. J. Gentry, Y. Yin, J. Liebich, T. C. Hazen and J. Zhou, “GeoChip 3.0 as a High Through-put Tool for Analyzing Microbial Community Composition, Structure and Functional Activity,” The ISME Journal, Vol. 4, No. 9, 2010, pp. 1167-1179. doi:10.1128/AEM.67.12.5780-5790.2001
[8]	S. Yamamoto and S. Harayama, “Phylogenetic Analysis of Pseudomonas Putida Strains Deduced from the Nucleotide Sequences of gyrB, rpoD, and 16S rRNA,” International Journal of Systematic Bacteriology, Vol. 48, No. 3, 1998, pp. 813-819. doi:10.1099/00207713-48-3-813
[9]	L. Wang, F. Lee, C. Tai, H. Kasai, “Comparison of gyrB Gene Sequences, 16S rRNA Gene Sequences and DNA-DNA Hybridization in the Bacillus Subtilis Group,” International Journal of Systematic and Evolutionary Microbiology, Vol. 57, No. 8, 2007, pp. 1846-1850. doi:10.1099/ijs.0.64685-0
[10]	Y. Liang, Z. He, L. Wu, Y. Deng, G. Li, J. Zhou, “Development of a Common Oligo Reference Standard (CORS) for Microarray Data Normalization and Comparison across Different Microbial Communities,” Applied and Environmental Microbiology, Vol. 76, No. 4, 2010, pp. 1088-1094. doi:10.1128/AEM.02749-09
[11]	M. B. Leigh, V. H. Pellizari, O. Uhlik, R. Sutka, J. Rodrigues, N. E. Ostrom, J. Zhou and J. M. Tiedje, “Biphenyl-Utilizing Bacteria and Their Functional Genes in a Pine Root Zone Contaminated with Polychlorinated Biphenyls (PCBs),” The ISME Journal, Vol. 1, No. 2, 2007, pp. 134-148. doi:10.1038/ismej.2007.26
[12]	J. Zhou, S. Kang, C. W. Schadt and C. T. Garten Jr., “Spatial Scaling of Functional Gene Diversity across Various Microbial Taxa,” Proceedings of National Academy of Science USA, Vol. 105, No. 22, 2008, pp. 7768-7773. doi:10.1073/pnas.0709016105
[13]	J. D. Van Nostrand, W. M. Wu, L. Wu, Y. Deng, J. Carley, S. Carroll, Z. He, B. Gu, J. Luo, C. S. Criddle, D. B. Watson, P. M. Jardine, T. L. Marsh, J. M. Tiedje, C. T. Hazen and J. Zhou, “GeoChip-Based Analysis of Functional Microbial Communities during the Reoxidation of a Bioreduced Uranium-Contaminated Aquifer,” Environmental Microbiology, Vol. 11, No. 10, 2009, pp. 2611-2626. doi:10.1111/j.1462-2920.2009.01986.x
[14]	Y. T. Liang, J. D. Van Nostrand, Y. Deng, Z. L. He, L. Y. Wu, Z. Xu, G. H. Li and J. Z. Zhou, “Functional Gene Diversity of Soil Microbial Communities from Five Oil-Contaminated Fields in China,” ISME Journal, Vol. 5, No. 3, 2011, pp. 403-413. doi:10.1038/ismej.2010.142
[15]	R. Atlas, “Microbial-Degradation of Petroleum Hydrocarbons: An Environmental Perspective,” Microbiological Review, Vol. 45, No. 1, 1981, pp. 180-209.
[16]	Y. Oh, D. Sim and S. Kim, “Effects of Nutrients on Crude Oil Biodegradation in the Upper Intertidal Zone,” Marine Pollutant Bulletin, Vol. 42, No. 12, 2001, pp. 1367-1372. doi:10.1016/S0025-326X(01)00166-7
[17]	S. K. Rhee, X. Liu, L. Wu, S. C. Chang, X. Wan and J. Zhou, “Detection of Genes Involved in the Biodegradation and Biotransformationin Microbial Community by Using 50 Mer Oligonucleotide Microarrays,” Applied and Environmental Microbiology, Vol. 70, No. 7, 2004, pp. 4303-4317. doi:10.1128/AEM.70.7.4303-4317.2004
[18]	E. Yergeau, S. Bokhorst, S. Kang, J. Zhou, C. W. Greer, R. Aerb and G. A. Kowalchuk, “Shifts in Soil Microorganisms in Response to Warming Are Consistent across a Range of Antarctic Environments,” ISME Journal, Vol. 6, No. 3, 2012, pp. 693-702. doi:10.1038/ismej.2011.124
[19]	L. Bodrossy, N. Stralis-Pavese, J. C. Murrell, S. Rasjwqaki, A. Weilharter and A. Sessitsch, “Development and Variation of a Diagnostic Microbial Microarray for Methanotrophs,” Environmental Microbiology, Vol. 5, No. 7, 2003, pp. 566-582. doi:10.1046/j.1462-2920.2003.00450.x
[20]	E. Yergeau, S. Kang, Z. He, J. Zhou and G. A. Kowalchuk, “Functional Microarray Analysis of Nitrogen and Carbon Cycling Genes across Antarctic Latitudinal Transect,” ISME Journal, Vol. 1, No. 2, 2007, pp. 163-179. doi:10.1038/ismej.2007.24
[21]	J. R. Reeve, C. W. Schadt, L. Carpenter-Boggs, S. Kang, J. Zhou and J. P. Reganold, “Effects of Soil Type and Farm Management on Soil Ecological Functional Gene and Microbial Activities,” ISME Journal, Vol. 4, No. 9, 2010, pp. 1099-1107. doi:10.1038/ismej.2010.42
[22]	L. Wu, X. Liu, C. W. Schadt and J. Zhou, “Microarray -Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification,” Applied and Environmental Microbiology, Vol. 72, No. 7, 2006, pp. 4931-4941. doi:10.1128/AEM.02738-05
[23]	T. J. Genty, G. S. Wickham, C. W. Schadt and J. Zhou, “Microarray Applications in Microbial Ecology Research,” Microbial Ecology, Vol. 52, No. 2, 2006, pp. 159-175. doi:10.1007/s00248-006-9072-6
[24]	H. Gao, Z. K. Yang, T. J. Gentry, L. Wu, C. W. Schadt and J. Zhou, “Microarray-Based Analysis of Microbial Community RNAs by Whole-Community RNA Amplification,” Applied and Environmental Microbiology, Vol. 73, No. 2, 2007, pp. 563-571. doi:10.1128/AEM.01771-06
[25]	S. E. Bulow, C. A. Francis, G. A. Jackson and B. B. Ward, “Sediment Denitrifier Community Composition and nirS Gene Expression Investigated with Functional Gene Microarrays,” Environmental Microbiology, Vol. 10, No. 11, 2008, pp. 3057-3069. doi:10.1111/j.1462-2920.2008.01765.x
[26]	E. L. Brodie, T. Z. DeSanti, D. C. Joyner, S. M. Baek and J. T. Larsen, “Application of a High Density Oligonucleotide Microarray Approach to Study Bacterial Population Dynamics during Uranium Reduction and ReOxidation,” Applied and Environmental Microbiology, Vol. 72, No. 9, 2006, pp. 6288-6298. doi:10.1128/AEM.00246-06
[27]	E. L. Brodie, T. Z. DeSantis, J. P. Parker, I. X. Zubiettza and Y. M. Piceno, “Uuban Aerosols Harbor Diverse and Dynamic Bacterial Population,” Proceedings of National Academy of Science USA, Vol. 104, No. 1, 2007, pp. 299-304. doi:10.1073/pnas.0608255104
[28]	A. Loy, A. Lehner, N. Lee, J. Adamczyk, H. Meier, J. Ernest, K. H. Schleifer and M. Wagner, “Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment,” Applied and Environmental Microbiology, Vol. 68, No. 10, 2002, pp. 5064-5081. doi:10.1128/AEM.68.10.5064-5081.2002
[29]	J. Peplies, O. F. Glockner and R. Amann, “Optimization Strategies for DNA Microarray-Based Detection of Bacteria with 16S rRNA Targeting Oligonucleotide Probes,” Applied and Environmental Microbiology, Vol. 69, No. 3, 2003, pp. 1397-1407. doi:10.1128/AEM.69.3.1397-1407.2003
[30]	M. Hery, H. Sanguin, F. S. Perez, T. M. Vogel, E. Paul and S. Alfenore, “Monitoring of Bacterial Communities during Low Temperature Thermal Treatment of Activated Sludge Combining DNA Phylochip and Respirometry Techniques,” Water Research, Vol. 44, No. 20, 2010, pp. 6133-6143. doi:10.1016/j.watres.2010.07.003
[31]	K. Cruz-Martinez, K. B. Suttle, E. L. Brodie, M. E. Power, G. L. Andersen and J. F. Banfield, “Despite Strong Seasonal Responses, Soil Microbial Consortia are More Resilient to Long-Term Changes in Rainfall than Overlying Grassland,” ISME Journal, Vol. 3, No. 6, 2009, pp. 738-744. doi:10.1038/ismej.2009.16
[32]	K. M. DeAngelis, E. L. Brodie, T. Z. DeSantis, G. L. Andersen, S. E. Lindow and M. K. Firestone, “Selective Progressive Response of Soil Microbial Community to Wild Oat Roots,” ISME Journal, Vol. 3, No. 2, 2009, pp. 168-178. doi:10.1038/ismej.2008.103
[33]	E. Yergeau, S. A. Schoondermark-Stolk , E. L. Brodie, S. Dejean, T. Z. DeSantis, O. Gonclaves, Y. M. Piceno, G. L. Andersen and G. A. Kowalchuk, “Environmental Microarray Analyses of Antarctic Soil Microbial Communities,” ISME Journal, Vol. 3, No. 3, 2009, pp. 340-351. doi:10.1038/ismej.2008.111
[34]	T. DeSantis, E. Brodie, J. Moberg, I. Zubieta, Y. Piceno and G. Andersen, “High-Density Universal 16Sr RNA Microarray Analysis Reveals Broader Diversity than Typical Clone Library When Sampling the Environment,” Microbial Ecology, Vol. 53, No. 3, 2007, pp. 371-383. doi:10.1007/s00248-006-9134-9
[35]	I. Franke-Whittle, S. Klammer and H. Insam, “Design and Application of an Oligonucleotide Microarray for the Investigation of Compost Microbial Communities,” Journal of Microbiological Methods, Vol. 62, No. 1, 2005, pp. 37-56. doi:10.1016/j.mimet.2005.01.008
[36]	H. He, Y. Piceno, Y. Deng, M. Xu, Z. Lu, T, DeSantis, G. Andersen, S. E. Hobbie, P. B. Reich and J. Zhou, “The Phylogenetic Composition and Structure of Soil Microbial Communities Shifts in Response to Elevated Carbon Dioxide,” ISME Journal, Vol. 6, No. 2, 2012, pp. 259-272. doi:10.1038/ismej.2011.99
[37]	D. Cheneby, A. Brauman, B. Rabary and L. Philippot, “Differential Responses of Nitrate Reducer Community Size, Structure and Activity to Tillage Systems,” Applied and Environmental Microbiology, Vol. 75, No. 10, 2009, pp. 3180-3186. doi:10.1128/AEM.02338-08
[38]	S. Hallin, C. M. Jones, M. Schloter and L. Philippot, “Relationship between N-Cycling Communities and Ecosystem Functioning in a 50-Year-Old Fertilization Experiment,” ISME Journal, Vol. 3, No. 5, 2009, pp. 597-605. doi:10.1038/ismej.2008.128
[39]	E. Yergeau, S. A. Schoondermark-Stolk, E. L. Brodie, S. Déjean, T. Z. DeSantis , O. Gon?alves, Y. M. Piceno, G. L. Andersen and G. A. Kowalchuk, “Environmental Microarray Analyses of Antarctic Soil Microbial Communities,” ISME Journal, Vol. 3, No. 3, 2009, pp. 340-351. doi:10.1038/ismej.2008.111
[40]	A. Engelbrektson, V. Kunin, K. C. Wrighton, N. Zvenigorodsky, F. Chen, H. Ochman and P. Hugenholtz, “Experimental Factors Affecting PCR-Based Estimates of Microbial Species Richness and Evenness,” ISME Journal, Vol. 4, No. 5, 2010, pp. 642-647. doi:10.1038/ismej.2009.153
[41]	M. T. Suzuki and S. J. Giovannoni, “Bias Caused by Template Annealing in the Amplification of Mixtures of 16S rRNA Genes by PCR,” Applied and Environmental Microbiology, Vol. 62, No. 2, 1996, pp. 625-630.
[42]	E. Yergeau, S. Kang, Z. He, J. Zhou and G.A. Kowalchuk, “Functional Microarray Analysis of Nitrogen and Carbon Cycling Genes across and Antarctic Latitudinal Transect,” ISME Journal, Vol. 1, No. 2, 2007, pp. 163-179. doi:10.1038/ismej.2007.24
[43]	J. Zhou, M. A. Bruns and J. M. Tiedje, “DNA Recovery from Soils of Diverse Composition,” Applied and Environmental Microbiology, Vol. 62, No. 2, 1996, pp. 316-322.