Impact of Different Methods of Soil Sampling and DNA Extraction on the Identification of Soil Bacterial Abundance under Elevated CO2

doi:10.4236/oalib.1103527

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Open Access Library Journal 4 2017

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Impact of Different Methods of Soil Sampling and DNA Extraction on the Identification of Soil Bacterial Abundance under Elevated CO₂

DOI: 10.4236/oalib.1103527, PP. 1-12

Fengxia Li, Saman Bowatte, Paul C. D. Newton, Dongwen Luo

Subject Areas: Soil Science, Agricultural Science

Keywords: DNA Extraction Kit, DNA Yield, DNA Quality, Gene Abundance, Bacterial 16S rRNA, Free Air Carbon Dioxide Enrichment

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Abstract

Elevated atmospheric CO₂ (eCO₂) is anticipated to have marked effects on soil microbial populations. While there is experimental evidence to support this view there are also studies where changes in microbial populations, such as the abundance of bacteria, are suggested but cannot be statistically established. We conducted this study to identify whether the sampling and sample treatment methods used could influence the results obtained using bacterial abundance as the variable of interest. We tested three different sampling methods and two different DNA extraction kits. The first because microbes are distributed heterogeneously in soil so the sampling procedure might be expected to influence the accuracy and precision of the population estimate and the second because the quantity and quality of DNA extracted influences the microbial analyses that can be performed and can introduce bias. Samples were taken from a long-running FACE experiment on grassland from under plants of Agrostis capillaris. We found that bacterial abundance was consistently lower under eCO₂ but we were only able to establish a statistical difference where a more intense sampling regime was used and bulking of the soil sample was avoided. A reduction in bacterial abundance is a consistent outcome in eCO₂ field experiments but the only other occasion where this reduction has been found to be significant was also where individual soil cores were analysed rather than the samples being bulked. We conclude that while there is extra work and cost attached to more detailed sampling this approach is highly desirable if we are to make robust conclusions about the impacts of eCO₂ on soil microbes.

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Li, F. , Bowatte, S. , Newton, P. C. D. and Luo, D. (2017). Impact of Different Methods of Soil Sampling and DNA Extraction on the Identification of Soil Bacterial Abundance under Elevated CO2. Open Access Library Journal, 4, e3527. doi: http://dx.doi.org/10.4236/oalib.1103527.

References

[1]	De Graaff, M.-A., Van Groenigen, K.-J., Six, J., Hungate, B. and Van Kessel, C. (2006) Interactions between Plant Growth and Soil Nutrient Cycling under Elevated CO2: A Meta-Analysis. Global Change Biology, 12, 2077-2091. https://doi.org/10.1111/j.1365-2486.2006.01240.x
[2]	Ross, D.J., Newton, P.C.D., Tate, K.R. and Luo, D. (2013) Impact of a Low Level of CO2 Enrichment on Soil Carbon and Nitrogen Pools and Mineralization Rates over Ten Years in a Seasonally Dry, Grazed Pasture. Soil Biology and Biochemistry, 58, 265-274. https://doi.org/10.1016/j.soilbio.2012.12.011
[3]	Sillen, W.M.A. and Dieleman, W.I.J. (2012) Effects of Elevated CO2 and N Fertilization on Plant and Soil Carbon Pools of Managed Grasslands: A Meta-Analysis. Biogeosciences, 9, 2247-2258.
[4]	Bloom, J.A., Burger, M., Kimball, B.A. and Pinter Jr., P. (2014) Nitrate Assimilation Is Inhibited by Elevated CO2 in Field-Grown Wheat. Nature Climate Change, 4, 477-480. https://doi.org/10.1038/nclimate2183
[5]	Gentile, R., Dodd, M., Lieffering, M., Brock, S.C., Theobald, P.W. and Newton, P.C.D. (2012) Effects of Long-Term Exposure to Enriched CO2 on the Nutrient-Supplying Capacity of a Grassland Soil. Biology and Fertility of Soils, 48, 357-362. https://doi.org/10.1007/s00374-011-0616-7
[6]	Myers, S.S., et al. (2014) Increasing CO2 Threatens Human Nutrition. Nature, 510, 139-142. https://doi.org/10.1038/nature13179
[7]	Reich, P.B. (2009) Elevated CO2 Reduces Losses of Plant Diversity Caused by nitrogen Deposition. Science, 326, 1399-1402. https://doi.org/10.1126/science.1178820
[8]	Hungate, B.A., et al. (2009) Assessing the Effect of Elevated Carbon Dioxide on Soil Carbon: A Comparison of Four Meta-Analyses. Global Change Biology, 15, 2020-2034. https://doi.org/10.1111/j.1365-2486.2009.01866.x
[9]	Schimel, J.P. and Bennett, J. (2004) Nitrogen Mineralization: Challenges of a Changing Paradigm. Ecology, 85, 591-602.
[10]	Van Der Heijden, M.G.A., Bardgett, R.D. and Van Straalen, N.M. (2008) The Unseen Majority: Soil Microbes as Drivers of Plant Diversity and Productivity in Terrestrial Ecosystems. Ecology Letters, 11, 296-310. https://doi.org/10.1111/j.1461-0248.2007.01139.x
[11]	Bowatte, S., Newton, P.C.D., Hill, A.M., Theobald, P., Luo, D., Hovenden, M. and Osanai, Y. (2013) Offspring of Plants Exposed to Elevated or Ambient CO2 Differ in Their Impacts on Soil Nitrification in a Common Garden Experiment. Soil Biology and Biochemistry, 62, 134-136.
[12]	Díaz, S., Grime, J.P., Harris, J. and McPherson, E. (1993) Evidence of a Feedback Mechanism Limiting Plant Response to Elevated Carbon Dioxide. Nature, 364, 616-617. https://doi.org/10.1038/364616a0
[13]	Hu, S., Tu, C., Chen, X. and Gruver, J.B. (2006) Progressive N Limitation of Plant Response to Elevated CO2: A Microbiological Perspective. Plant and Soil, 289, 47-58. https://doi.org/10.1007/s11104-006-9093-4
[14]	Singh, B.K., Bardgett, R.D., Smith, P. and Reay, D.S. (2010) Microorganisms and Climate Change: Terrestrial Feedbacks and Mitigation Options. Nature Reviews Microbiology, 8, 779-790. https://doi.org/10.1038/nrmicro2439
[15]	Zak, D.R., Pregitzer, K.S., King, J.S. and Holmes, W.E. (2000) Elevated Atmospheric CO2, Fine Roots and the Response of Soil Microorganisms: A Review and Hypothesis. New Phytologist, 147, 201-222. https://doi.org/10.1046/j.1469-8137.2000.00687.x
[16]	Jossi, M., Fromin, N., Tarnawski, S., Kohler, F., Gillet, F., Aragno, M. and Hamelin, J. (2006) How Elevated pCO2 Modifies Total and Metabolically Active Bacterial Communities in the Rhizosphere of Two Perennial Grasses Grown under Field Conditions. FEMS Microbiology Ecology, 55, 339-350. https://doi.org/10.1111/j.1574-6941.2005.00040.x
[17]	Baker, K.L., Langenheder, S., Nicol, G.W., Ricketts, D., Killham, K., Campbell, C.D. and Prosser, J.I. (2009) Environmental and Spatial Characterisation of Bacterial Community Composition in Soil to Inform Sampling Strategies. Soil Biology and Biochemistry, 41, 2292-2298.
[18]	Kirk, J.L., Beaudette, L.A., Hart, M., Moutoglis, P., Klironomos, J.N., Lee, H. and Trevors, J.T. (2004) Methods of Studying Soil Microbial Diversity. Journal of Microbiological Methods, 58, 169-188.
[19]	Lombard, N., Prestat, E., van Elsas, J.D. and Simonet, P. (2011) Soil-Specific Limitations for Access and Analysis of Soil Microbial Communities by Metagenomics. FEMS Microbiology Ecology, 78, 31-49. https://doi.org/10.1111/j.1574-6941.2011.01140.x
[20]	Carrigg, C., Rice, O., Kavanagh, S., Collins, G. and O’Flaherty, V. (2007) DNA Extraction Method Affects Microbial Community Profiles from Soils and Sediment. Applied Microbiology and Biotechnology, 77, 955-964. https://doi.org/10.1007/s00253-007-1219-y
[21]	Leite, D.C.A., Balieiro, F.C., Pires, C.A., Madari, B.E., Rosado, A.S., Coutinho, H.L.C. and Peixoto, R.S. (2014) Comparison of DNA Extraction Protocols for Microbial Communities from Soil Treated with Biochar. Brazilian Journal of Microbiology, 45, 175-183. https://doi.org/10.1590/S1517-83822014000100023
[22]	Newton, P.C.D., Allard, V., Carran, R.A. and Lieffering, M. (2006) Impacts of Elevated CO2 on a Grassland Grazed by Sheep: The New Zealand FACE Experiment. In: Nosberger, J., Long, S.P., Norby, R.J., Stitt, M., Hendrey, G.R. and Blum, H., Eds., Managed Ecosystems and CO2: Case Studies, Processes, and Perspectives. Ecological Studies: Analysis and Synthesis, Vol. 187, Springer-Verlag, Berlin, 157-171. https://doi.org/10.1007/3-540-31237-4_9
[23]	Castro, H.F., Classen, A.T., Austin, E.E., Norby, R.J. and Schadt, C.W. (2010) Soil Microbial Community Responses to Multiple Experimental Climate Change Drivers. Applied and Environmental Microbiology, 76, 999-1007. https://doi.org/10.1128/AEM.02874-09
[24]	Dunbar, J., Gallegos-Graves, L.V., Steven, B., Mueller, R., Hesse, C., Zak, D.R. and Kuske, C.R. (2014) Surface Soil Fungal and Bacterial Communities in Aspen Stands Are Resilient to Eleven Years of Elevated CO2 and O3. Soil Biology and Biochemistry, 76, 227-234.
[25]	Haugwitz, M., Bergmark, L., Priemé, A., Christensen, S., Beier, C. and Michelsen, A. (2014) Soil Microorganisms Respond to Five Years of Climate Change Manipulations and Elevated Atmospheric CO2 in a Temperate Heath Ecosystem. Plant and Soil, 374, 211-222. https://doi.org/10.1007/s11104-013-1855-1
[26]	Hayden, H.L., et al. (2012) Changes in the Microbial Community Structure of Bacteria, Archaea and Fungi in Response to Elevated CO2 and Warming in an Australian Native Grassland Soil. Environmental Microbiology, 14, 3081-3096. https://doi.org/10.1111/j.1462-2920.2012.02855.x
[27]	Oppermann, B.I., et al. (2010) Soil Microbial Community Changes as a Result of Long-Term Exposure to a Natural CO2 Vent. Geochimica et Cosmochimica Acta, 74, 2697-2716.
[28]	Newton, P.C.D., et al. (2014) Selective Grazing Modifies Previously Anticipated Responses of Plant Community Composition to Elevated CO2 in Temperate Grassland. Global Change Biology, 20, 158-169. https://doi.org/10.1111/gcb.12301
[29]	Edwards, G., Clark, H. and Newton, P.C.D. (2001) The Effects of Elevated CO2 on Seed Production and Seedling Recruitment in a Sheep-Grazed Pasture. Oecologia, 127, 383-394. https://doi.org/10.1007/s004420000602
[30]	Harris, W. and Brougham, R.W. (1968) Some Factors Affecting Change in Botanical Composition in a Ryegrass-White Clover Pasture under Continuous Grazing. New Zealand Journal of Agricultural Research, 11, 15-38. https://doi.org/10.1080/00288233.1968.10431631
[31]	Allard, V., Newton, P.C.D., Lieffering, M., Clark, H., Matthew, C., Soussana, J.F. and Gray, Y.S. (2003) Nitrogen Cycling in Grazed Pastures at Elevated CO2: N Returns by Ruminants. Global Change Biology, 9, 1731-1742. https://doi.org/10.1111/j.1365-2486.2003.00711.x
[32]	Cornforth, I.S. and Sinclair, A.G. (1984) Fertiliser and Lime Recommendations for Pastures and Crops in New Zealand. 2nd Revised Edition, Ministry of Agriculture and Fisheries, Wellington.
[33]	Pirondini, A., Bonas, U., Maestri, E., Visioli, G., Marmiroli, M. and Marmiroli, N. (2010) Yield and Amplificability of Different DNA Extraction Procedures for Traceability in the Dairy Food Chain. Food Control, 21, 663-668.
[34]	Quigley, L., O’Sullivan, O., Beresford, T.P., Paul Ross, R., Fitzgerald, G.F. and Cotter, P.D. (2012) A Comparison of Methods Used to Extract Bacterial DNA from Raw Milk and Raw Milk Cheese. Journal of Applied Mi-crobiology, 113, 96-105. https://doi.org/10.1111/j.1365-2672.2012.05294.x
[35]	Heuer, H., Krsek, M., Baker, P., Smalla, K. and Wellington, E.M.H. (1997) Analysis of Actinomycete Communities by Specific Amplification of Genes Encoding 16S rRNA and Gel-Electrophoretic Separation in Denaturing Gradients. Applied and Environmental Microbiology, 63, 3233-3241.
[36]	Yates, M.D., et al. (2012) Convergent Development of Anodic Bacterial Communities in Microbial Fuel Cells. ISME Journal, 6, 2002-2013. https://doi.org/10.1038/ismej.2012.42
[37]	Pinheiro, J., Bates, D., DebRoy, S. and Sarkar, D. (2013) nlme: Linear and Nonlinear Mixed Effects Models. R Package Version 3.1-109. R Foundation for Statistical Computing.
[38]	Vishnivetskaya, T.A., et al. (2014) Commercial DNA Extraction Kits Impact Observed Microbial Community Composition in Permafrost Samples. FEMS Microbiology Ecology, 87, 217-230. https://doi.org/10.1111/1574-6941.12219
[39]	Hazen, T.C., Rocha, A.M. and Techtmann, S.M. (2013) Advances in Monitoring Environmental Microbes. Current Opinion in Biotechnology, 24, 526-533.
[40]	Feinstein, L.M., Woo, J.S. and Blackwood, C.B. (2009) Assessment of Bias Associated with Incomplete Extraction of Microbial DNA from Soil. Applied and Environmental Microbiology, 75, 5428-5433. https://doi.org/10.1128/AEM.00120-09
[41]	Fortin, N., Beaumier, D., Lee, K. and Greer, C.W. (2004) Soil Washing Improves the Recovery of Total Community DNA from Polluted and High Organic Content Sediments. Journal of Microbiological Methods, 56, 181-191.
[42]	Ge, Y., Chen, C., Xu, Z., Oren, R. and He, J.Z. (2010) The Spatial Factor, Rather than Elevated CO2, Controls the Soil Bacterial Community in a Temperate Forest Ecosystem. Applied and Environmental Microbiology, 76, 7429-7436. https://doi.org/10.1128/AEM.00831-10

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