AS  Vol.10 No.3 , March 2019
Changes in Soil Microbial Activity and Community Composition as a Result of Selected Agricultural Practices
For a constantly growing human population, healthy and productive soil is critical for sustainable delivery of agricultural products. The soil microorganisms play a crucial role in soil structure and functioning. They are responsible for soil formation, ecosystem biogeochemistry, cycling of nutrients and degradation of plant residues and xenobiotics. Certain agricultural treatments, such as fertilizers and pesticides applications, crop rotation, or soil amendment addition, influence the composition, abundance and function of bacteria and fungi in the soil ecosystems. Some of these practices have rather negative effects; others can help soil microorganisms by creating a friendlier habitat or providing nutrients. The changes in microbial community structure cannot be fully captured with traditional methods that are limited only to culturable organisms, which represent less than 1% of the whole population. The use of new molecular techniques such as metagenomics offers the possibility to better understand how agriculture affects soil microbiota. Therefore, the main goal of this review is to discuss how common farming practices influence microbial activity in the soil, with a special focus on pesticides, fertilizers, heavy metals and crop rotation. Furthermore, potential practices to mitigate the negative effects of some treatments are suggested and treatments that can beneficially influence soil microbiota are pointed out. Finally, application of metagenomics technique in agriculture and perspectives of developing efficient molecular tools in order to assess soil condition in the context of microbial activities are underlined.
Cite this paper
Głodowska, M. and Wozniak, M. (2019) Changes in Soil Microbial Activity and Community Composition as a Result of Selected Agricultural Practices. Agricultural Sciences, 10, 330-351. doi: 10.4236/as.2019.103028.
[1]   Keesstra, S., Nunes, J., Novara, A., Finger, D., Avelar, D., Kalantari, Z. and Cerdà, A. (2018) The Superior Effect of Nature-Based Solutions in Land Management for Enhancing Ecosystem Services. Science of the Total Environment, 610, 997-1009.

[2]   Buckley, D.H. and Schmidt, T.M. (2001) The Structure of Microbial Communities in Soil and the Lasting Impact of Cultivation. Microbial Ecology, 42, 11-21.

[3]   Nielsen, S., Minchin, T., Kimber, S., Zwieten, L., Gilbertd, J., Munroe, P., Joseph, S. and Thomas, T. (2014) Comparative Analysis of the Microbial Communities in Agricultural Soil Amended with Enhanced Biochars or Traditional Fertilizers. Agriculture, Ecosystems and Environment, 191, 73-82.

[4]   Hafez, H.F.H. and Theimann, W.H.P. (2003) Persistence and Biodegradation of Iazinone and Imidacloprid in Soil. XII Symposium Pesticide Chemistry, Piacenza, 2003, 35-42.

[5]   Smith, S.E. and Smith, F.A. (2012) Fresh Perspectives on the Roles of Arbuscular Mycorrhizal Fungi in Plant Nutrition and Growth. Mycologia, 104, 1-13.

[6]   Mohammadi, K. (2012) Phosphorus Solubilizing Bacteria, Occurrence, Mechanisms and Their Role in Crop Production. Resources and Environment, 2, 80-85.

[7]   Brussaard, L. (1997) Biodiversity and Ecosystem Functioning in Soil. Ambio, 26, 563-570.

[8]   Tisdall, J. (1994) Possible Role of Soil Microorganisms in Aggregation in Soils. Plant and Soil, 159, 115-121.

[9]   Susilo, F.X., Neutel, A.M., van Noordwijk, M., Hairiah, K., Brown, G. and Swift, M.J. (2004) Soil Biodiversity and Food Webs. In: van Noordwijk, M., Cadisch, G. and Ong, C.K., Eds., Below-Ground Interactions in Tropical Agroecosystems, CAB International, Wallingford, 285-302.

[10]   Haas, D. and Défago, G. (2005) Biological Control of Soil-Borne Pathogens by Fluorescent Pseudomonads. Nature Reviews in Microbiology, 3, 307-319.

[11]   Bhat, A.K. (2013) Preserving Microbial Diversity of Soil Ecosystem: A Key to Sustainable Productivity. International Journal of Current Microbiology and Applied Sciences, 2, 85-101.

[12]   Bernard, B., Larkin, R.P., Tavantzis, S., Erich, M.S., Alyokhin, A., Sewell, G., Lannan, A. and Gross, S.D. (2012) Compost, Rapeseed Rotation, and Biocontrol Agents Significantly Impact Soil Microbial Communities in Organic and Conventional Potato Production Systems. Applied Soil Ecology, 52, 21-49.

[13]   Lazcano, C., Gómez-Brandón, M. and Revilla P. (2013) Short-Term Effects of Organic and Inorganic Fertilizers on Soil Microbial Community Structure and Function. A Field Study with Sweet Corn. Biology and Fertility of Soils, 49, 723-733. DOI:

[14]   Zhong, W., Gu, T., Wang, W., Zhang, B., Lin, X., Huang, Q. and Shen, W. (2010) The Effects of Mineral Fertilizer and Organic Manure on Soil Microbial Community and Diversity. Plant and Soil, 326, 511-522.

[15]   Lauber, C.L., Hamady, M., Knight, R. and Fierer, N. (2009) Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale. Applied and Environmental Microbiology, 75, 5111-5120.

[16]   Gans, J., Woilinsky, M. and Dunbar, J. (2005) Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil. Science, 309, 1387-1390.

[17]   Bell, T., Newman, J.A., Silverman, B.W., Turner S.L. and Lilley, A.K. (2005) The Contribution of Species Richness and Composition to Bacterial Services. Nature, 436, 1157-1160.

[18]   Miller, D.N., Bryant, J.E., Madsen, E.L. and Ghiorse, W.C. (1999) Evaluation and Optimization of DNA Extraction and Purification Procedures for Soil and Sediment Samples. Applied and Environmental Microbiology, 65, 4715-4724.

[19]   Kennedy, A.C. and Smith, K.L. (1995) Soil Microbial Diversity and the Sustainability of Agricultural Soils. Plant and Soil, 170, 75-86.

[20]   Martyniuk, S. and Wagner, G.H. (1978) Quantitative and Qualitative Examination of Soil Microflora Associated with Different Management Systems. Soil Science, 125, 343-350.

[21]   Han, W., Kemmitt, S.J. and Brookes, P.C. (2007) Soil Microbial Biomass and Activity in Chinese Tea Gardens of Varying Stand Age and Productivity. Soil Biology and Biochemistry, 39, 1468-1478.

[22]   Handa, S.K., Agnihotri, N.P. and Kulshrestha, G. (1999) Maximum Residue Limits of Pesticides. In: Handa, S.K., Agnihotri, N.P. and Kulshrestha, G., Eds., Pesticide Residues Significance, Management and Analysis, Research Periodicals and Book Publishing House, Houston, 184-198.

[23]   Fenner, K., Canonica, S., Wackett, L.P. and Elsner, M. (2013) Evaluating Pesticide Degradation in the Environment, Blind Spots and Emerging Opportunities. Science, 341, 752-758.

[24]   Chowdhury, A., Pradhan, S., Saha, M. and Sanya, N. (2008) Impact of Pesticides on Soil Microbiological Parameters and Possible Bioremediation Strategies. Indian Journal of Microbiology, 48,114-127.

[25]   Moorman, T.B. and Harper, S.S. (1989) Transformation and Mineralization of Metribuzin in Surface and Subsurface Horizons of a Mississippi Delta Soil. Journal of Environmental Quality, 18, 302-306.

[26]   Torstenssen, L. and Stenstorm, J. (1986) Basic Respiration Rate as a Tool for Prediction of Pesticide Persistence in Soil. Environmental Toxicology, 1, 57-72.

[27]   Voos, G. and Groffman, P.M. (1997) Relationship between Microbial Biomass and Dissipation of 2, 4-D and Dicamba in Soil. Biology and Fertility of Soils, 24, 106-110.

[28]   Walker, A., Moon, Y.H. and Welch, S.J. (1992) Influence of Temperature, Soil Moisture and Soil Characteristics on Persistence of Alachlor. Journal of Pest Science, 35,109-116.

[29]   Anderson, J.P.E. (1981) Methods to Evaluate Pesticide Damage to the Biomass of the Soil Microflora. Soil Biology and Biochemistry, 13, 149-153.

[30]   Duah-Yentumi, S. and Johnson, D.B. (1986) Changes in Soil Microflora in Response to Repeated Applications of Some Pesticides. Soil Biology and Biochemistry, 18, 629-635.

[31]   Wardle, D.A. and Parkinson, D. (1992) The Influence of the Herbicide Glyphosate on Interspecific Interactions between Four Soil Fungal Species. Mycological Research, 24, 185-186.

[32]   Perucci, P. and Scarponi, L. (1994) Effects of the Herbicide Imazethapyr on Soil Microbial Biomass and Various Soil Enzyme Activities. Biology and Fertility of Soils, 17, 237-240.

[33]   Rath, A.K., Ramakrishnan, B., Kumaraswamy, S., Bharati, K., Singla, P. and Sethunathan, N. (1998) Effect of Pesticides on Microbial Biomass of Flooded Soil. Chemosphere, 37, 661-671.

[34]   Vischetti, C., Perucci, P. and Scarponi, L. (2000) Relationship between Rimusulfuron Degradation and Microbial Biomass Content in a Clay Loam Soil. Biology and Fertility of Soils, 31, 310-314.

[35]   Araújo, A.S.F., Monterio, R.T.R. and Abarkeli, R.B. (2003) Effect of Glyphosate on the Microbial Activity of Two Brazilian Soils. Chemosphere, 52, 799-804.

[36]   Lundgren, B. (1981) Fluorescein Diacetate as a Stain of Metabolically Active Bacteria in Soil. Oikos, 36, 17-22.

[37]   Zelles, L., Scheunert, I. and Korte, F. (1985) Side Effects of Some Pesticides on Non-Target Soil Microorganisms. Journal of Environmental Science and Health, 20, 457-488.

[38]   Pankhurst, C.E., Hawke, B.A., McDonald, H.J., Kirby, C.A., Buckerfield, J.C., Michelsen, P.U., Brien, K.A., Gupta, V.V.S.R. and Doube, B.M. (1995) Evaluation of Soil Biological Properties as Potential Bioindicators of Soil Health. Australian Journal of Experimental Agriculture, 35, 1015-1028.

[39]   Yao, X.-H., Min, H., Lü, Z.-H. and Yuan, H.-P. (2006) Influence of Acetamiprid on Soil Enzymatic Activities and Respiration. European Journal of Soil Biology, 42, 120-126.

[40]   Bartha, R., Lanzilotta, R.P. and Pramer, D. (1967) Stability and Effects of Some Pesticides in Soil. Journal of Applied Microbiology, 15, 67-75.

[41]   Tu, C.M. (1992) Effect of Some Herbicides on Activities of Microorganisms and Enzymes in Soil. Journal of Environmental Science and Health, 27, 695-709.

[42]   Haney, R.L., Senseman, S.A., Hons, F.M. and Zuberer, D.A. (2000) Effect of Glyphosate on Soil Microbial Activity and Biomass. Weed Science, 48, 89-93.

[43]   Gomez, E., Ferreras, L., Lovotti, L. and Fernandez, E. (2009) Impact of Glyphosate Application on Microbial Biomass and Metabolic Activity in a Vertic Argiudoll from Argentina. European Journal of Soil Biology, 45, 163-167.

[44]   Sebiomo, A., Ogundero, V.W. and Bankole, S.A. (2011) Effect of Four Herbicides on Microbial Population, Soil Organic Matter and Dehydrogenase Activity. African Journal of Biotechnology, 10, 770-778.

[45]   Milenkovski, S., Bååth, E., Lindgren, P.E. and Berglund, O. (2010) Toxicity of Fungicides to Natural Bacterial Communities in Wetland Water and Sediment Measured Using Leucine Incorporation and Potential Denitrification. Ecotoxicology, 19, 285-294.

[46]   Zhuang, R.S., Chen, H.L., Yao, J., Li, Z., Burnet, J.E. and Choi, M.M.F. (2011) Impact of Beta-Cypermethrin on Soil Microbial Community Associated with Its Bioavailability, a Combined Study by Isothermal Microcalorimetry and Enzyme Assay Techniques. Journal of Hazardous Materials, 189, 323-328.

[47]   Goswami, M.R., Pati, U.K., Chowdhury, A. and Mukhopadhyay, A. (2013) Studies on the Effect of Cypermethrin on Soil Microbial Biomass and Its Activity in an Alluvial Soil. Journal of the Science of Food and Agriculture, 3, 1-9.

[48]   Beelen, P.V. and Doelman, P. (1997) Significance and Application of Microbial Toxicity Tests in Assessing Ecotoxicological Risks of Contaminants in Soil and Sediment. Chemosphere, 34, 455-499.

[49]   Anderson, T.H. and Domsch, K.H. (1990) Application of Ecophysiological Quotients (qCO2 and qD) on Microbial Biomass from Soils of Different Cropping Histories. Soil Biology and Biochemistry, 22, 251-255.

[50]   Jones, W.J. and Ananyeva, N.D. (2001) Correlations between Pesticide Transformation Rate and Microbial Respiration Activity in Soil of Different Ecosystems. Biology and Fertility of Soils, 33,477-483.

[51]   Moreno, J.L., Aliaga, A., Navarro, S., Hernandez, T. and Garcia, C. (2007) Effects of Atrazine on Microbial Activity in Semiarid Soil. Applied Soil Ecology, 35, 120-127.

[52]   Zhang, B.G., Bai, Z.H., Hoefel, D., Tang, L., Wang, X.Y., Li, B.J., Li, Z.M. and Zhuang, G.Q. (2009) The Impacts of Cypermethrin Pesticide Application on the Non-Target Microbial Community of the Pepper Plant Phillosphere. Science of the Total Environment, 407, 1915-1922.

[53]   Bælum, J., Nicolaisen, M.H., Holben, W.E., Strobel, B.W., Sørensen, J. and Jacobsen, C.S. (2008) Direct Analysis of tfdA Gene Expression by Indigenous Bacteria in Phenoxy Acid Amended Agricultural Soil. The ISME Journal, 2, 677-687.

[54]   Savci, S. (2012) An Agricultural Pollutant: Chemical Fertilizer International. Journal of Environmental Science and Development, 3, 77-80.

[55]   Swift, M.J., Heal, O.J. and Anderson, J.M. (1979) Decomposition in Terrestrial Ecosystems. Blackwell, Oxford.

[56]   Bhoi, L. and Mishra, P.C. (2012) Changes in Bacterial Density, CO2 Evolution and Enzyme Activities in Poultry Dung Amended Soil. Open Journal of Soil Science, 2, 196-201.

[57]   Bol, R., Kandeler, E., Amelung, W., Glaser, B., Marx, M.C., Preedy, N. and Lorenz, K. (2003) Short-Term Effects of Dairy Slurry Amendment on Carbon Sequestration and Enzyme Activities in a Temperate Grassland. Soil Biology and Biochemistry, 35, 1411-1421.

[58]   Allison, S.D. and Martiny, J.B.H. (2008) Resistance, Resilience, and Redundancy in Microbial Communities. Proceedings of the National Academy of Sciences of the United States of America, 105, 11512-11519.

[59]   Treseder, K.K. (2008) Nitrogen Additions and Microbial Biomass: A Meta-Analysis of Ecosystem Studies. Ecology Letters, 11, 1111-1120.

[60]   Omar, S.A. and Ismail, M. (1999) Microbial Populations, Ammonification and Nitrification in Soil Treated with Urea and Inorganic Salts. Folia Microbiologica, 44, 205-212.

[61]   Geisseler, D. and Scow, K.M. (2014) Long-Term Effects of Mineral Fertilizers on Soil Microorganisms—A Review. Soil Biology and Biochemistry, 75, 54-63.

[62]   Fierer, N. and Jackson, R.B. (2006) The Diversity and Biogeography of Soil Bacterial Communities. Proceedings of the National Academy of Sciences, 103, 626-631.

[63]   Russell, A.E.L.D. (2006) Nitrogen Fertilization and Cropping System Impacts on Soil Quality in Midwestern Mollisols. Soil Science Society of America Journal, 1, 249-255.

[64]   Zhou, J., Xia, F., Liu, X.M., He, Y., Xu, J.M. and Brookes, P.C. (2014) Effects of Nitrogen Fertilizer on the Acidification of Two Typical Acid Soils in South China. Journal of Soils and Sediments, 14, 415-422.

[65]   Vieira, F., Bayer, C., Mielniczuk, J., Zanatta, J. and Bissani, C.A. (2008) Long-Term Acidification of a Brazilian Acrisol as Affected by No Till Cropping Systems and Nitrogen Fertilizer. Australian Journal of Soil Research, 46, 17-26.

[66]   Juo, A.S.R., Dabiri, A. and Franzluebbers, K. (1995) Acidification of a Kaolinitic Alfisol under Continuous Cropping with Nitrogen Fertilization in West Africa. Plant and Soil, 171, 245-253.

[67]   Haynes, R.J. and Naidu, R. (1998) Influence of Lime, Fertilizer and Manure Applications on Soil Organic Matter Content and Soil Physical Conditions: A Review. Nutrient Cycling in Agroecosystems, 51, 123-137.

[68]   Saito, M. and Marumoto, T. (2002) Inoculation with Arbuscular Mycorrhizal Fungi: the Status Quo in Japan and the Future Prospects. In: Diversity and Integration in Mycorrhizas, Springer, Dordrecht, 273-279.

[69]   Glodowska, M., Husk, B., Schwinghamer, T. and Smith, D. (2016) Biochar Is a Growth-Promoting Alternative to Peat Moss for the Inoculation of Corn with a Pseudomonad. Agronomy for Sustainable Development, 36, 21.

[70]   Anderson, C.R., Condrona, L.M., Clough, T., Fiers, M., Stewart, A., Hill, R.A. and Sherlock, R.R. (2011) Biochar Induced Soil Microbial Community Change: Implications for Biogeochemical Cycling of Carbon, Nitrogen and Phosphorus. Pedobiologia, 54, 309-320.

[71]   Zimmerman, A.R. (2010) Abiotic and Microbial Oxidation of Laboratory-Produced Black Carbon (Biochar). Environmental Science & Technology, 44, 1295-1301.

[72]   Adesemoye, A.O., Torbert, H.A. and Kloepper, J.W. (2009) Plant Growth-Promoting Rhizobacteria Allow Reduced Application Rates of Chemical Fertilizers. Microbial Ecology, 85, 1-12.

[73]   Vázquez, M.M., César, S., Azcón, R. and Barea, R.M. (2000) Interactions between Arbuscular Mycorrhizal Fungi and Other Microbial Inoculants (Azospirillum, Pseudomonas, Trichoderma) and Their Effects on Microbial Population and Enzyme Activities in the Rhizosphere of Maize Plants. Applied Soil Ecology, 15, 261-272.

[74]   Elsas, J.D., Duarte, G.F., Rosado, A.S. and Smalla, K. (1998) Microbiological and Molecular Biological Methods for Monitoring Microbial Inoculants and Their Effects in the Soil Environment. Journal of Microbiological Methods, 32, 133-154.

[75]   Nicholson, F.A., Smith, S.R., Alloway, B.J., Carlton-Smith, C. and Chambers, B.J. (2003) An Inventory of Heavy Metals Inputs to Agricultural Soils in England and Wales. Science of the Total Environment, 311, 205-219.

[76]   Babich, H. and Stotzky, G. (1980) Environmental Factors That Influence the Toxicity of Heavy Metal and Gaseous Pollutants to Microorganisms. RC Critical Reviews in Microbiology, 8, 99-145.

[77]   Donkova, R. and Kaloyanova, N. (2008) The Impact of Soil Pollutants on Soil Microbial Activity. In: Simeonov, L. and Sargsyan, V., Eds., Soil Chemical Pollution, Risk Assessment, Remediation and Security, NATO Science for Peace and Security Series, Springer, Dordrecht.

[78]   Donkova, R. and Dinev, N. (2006) Microbiological Characteristic of Soils in the Area of Nonferrous Metals Factory, Town of Plovdiv, Bulgaria. 11th Congress of the Microbiologists in Bulgaria, Varna, 2006.

[79]   Wang, M. and Zhou, Q. (2006). Effects of Herbicide Chlorimuron-Ethyl on Physiological Mechanisms in Wheat (Triticum aestivum). Ecotoxicology and Environmental Safety, 64, 190-197.

[80]   Maliszewska-Kordybach, B. and Smreczak, B. (2003) Habitat Function of Agricultural Soils as Affected by Heavy Metals and Polycyclic Aromatic Hydrocarbons Contamination. Environment International, 28, 719-728.

[81]   Giller, K.E., Nussbaum, R., Chaudri, A.M. and McGrath, S.P. (1993) Rhizobium meliloti Is Less Sensitive to Heavy Metal Contamination in Soil than R. leguminosarum bv. trifolii or R. loti. Soil Biology and Biochemistry, 25, 273-278.

[82]   Giller, K.E., Witter, E. and Mcgrath, S.P. (1998) Toxicity of Heavy Metals to Microorganisms and Microbial Processes in Agricultural Soils: A Review. Soil Biology and Biochemistry, 30, 1389-1414.

[83]   Nihorimbere, V., Ongena, M., Smargiassi, M. and Thonart, P. (2011) Beneficial Effect of the Rhizosphere Microbial Community for Plant Growth and Health. Biotechnology, Agronomy, Society and Environment, 15, 327-337.

[84]   Steenhoudt, O. and Vanderleyden, J. (2000) Azospirillum, a Free-Living Nitrogen-Fixing Bacterium Closely Associated with Grasses: Genetic, Biochemical and Ecological Aspects. FEMS Microbiology Reviews, 24, 487-506.

[85]   Zak, D.R., Holmes, W.E., White, D.C., Peascock A.D. and Tilman, D. (2003) Plant Diversity, Soil Microbial Communities and Ecosystem Function: Are There Any Links? Ecology, 84, 2042-2050.

[86]   Carney, K.M. and Matson, P.A. (2005) Plant Communities, Soil Microorganisms, and Soil Carbon Cycling: Does Altering the World Belowground Matter to Ecosystem Functioning? Ecosystems, 8, 928-940.

[87]   Spehn, E.M., Joshi, J., Schmid, B., Alphei, J. and Körner, C. (2000) Plant Diversity Effects on Soil Heterotrophic Activity in Experimental Grassland Ecosystems. Plant and Soil, 224, 217-230.

[88]   Scherer-Lorenzen, M., Palmborg, C., Prinz, A. and Schulze, E.D. (2003) The Role of Plant Diversity and Composition for Nitrate Leaching in Grasslands. Ecology, 84, 1539-1552.[1539:TROPDA]2.0.CO;2

[89]   Wardle, D.A., Bardgett, R.D. and Klironomos, J.N. (2004) Ecological Linkages between Aboveground and Belowground Biota. Science, 304, 1629-1633.

[90]   Trivedi, P., Pandey, A. and Palni, L.M.S. (2005) Carrier-Based Preparations of Plant Growth-Promoting Bacterial Inoculants Suitable for Use in Cooler Regions. World Journal of Microbiology and Biotechnology, 21, 941-945.

[91]   Jordan, D.C. (1984) Family III. Rhizobiaceae Conn 1938. In: Krieg, N.R. and Holt, J.C.., Eds., Bergey’s Manual of Systematic Bacteriology, Williams and Wilkins, Baltimore, ND.

[92]   Segovia, L., Young, J.P.W. and Martinez-Romero, E. (1993) Reclassification of American Rhizobium leguminosarum Biovar Phaseoli Type 1 Strains as Rhizobium etli sp. nov. International Journal of Systematic and Evolutionary Microbiology, 43, 374-377.

[93]   Morgan, J.A.W., Bending, G.D. and White, P.J. (2005) Biological Costs and Benefits to Plant—Microbe Interactions in the Rhizosphere. Journal of Experimental Botany, 56, 1729-1739.

[94]   Bending, G.D. (2003) The Rhizosphere and Its Microorganisms. In: Thomas, B., Murphy, D.J. and Murray, B.G., Eds., Encyclopaedia of Applied Plant Sciences, Academic Press, London, 1123-1129.

[95]   Brimecombe, M.J., De Leij, F.A. and Lynch, J.M. (2001) The Effect of Root Exudates on Rhizosphere Microbial Populations. In: Pinto, R., Varanini, Z. and Nannipierei, P., Eds., The Rhizosphere, Marcel Dekker, New York, 95-141.

[96]   Bhattacharyya, P.N. and Jha, D.K. (2011) Plant Growth-Promoting Rhizobacteria (PGPR): Emergence in Agriculture. World Journal of Microbiology and Biotechnology, 28, 1327.

[97]   Yang, C.H., Crowley, D.E. and Menge, J.A. (2001) 16S rDNA Fingerprinting of Rhizosphere Bacterial Communities Associated with Healthy and Phytophthora Infected Avocado Roots. FEMS Microbiology Ecology, 35, 129-136.

[98]   Hilton, S., Bennett, A.J., Keane, G., Bending, G.D., Chandler, D., Stobart, R. and Mills, P. (2013) Impact of Shortened Crop Rotation of Oilseed Rape on Soil and Rhizosphere Microbial Diversity in Relation to Yield Decline. PLoS ONE, 8, e59859.

[99]   Jiang, Y.J., Liang, Y.T., Li, C.M., Wang, F., Sui, Y.Y., Suvannang, N., Zhou, J.Z. and Sun, B. (2016) Crop Rotations Alter Bacterial and Fungal Diversity in Paddy Soils across East Asia. Soil Biologyand Biochemistry, 95, 250-261.

[100]   Milling, A., Smalla, K, Maidl, F.X., Schloter, M. and Munch, J.C. (2004) Effects of Transgenic Potatoes with an Altered Starch Composition on the Diversity of Soil and Rhizosphere Bacteria and Fungi. Plant Soil, 266, 23-39.

[101]   Sessitsch, A., Gyamfi, S., Tscherko, D., Gerzabek, M.H. and Kandeler, E. (2005) Activity of Microorganisms in the Rhizosphere of Herbicide Treated and Untreater Transgenic Glufosinate-Tolerant and Wildtype Oilseed Rape Grown in Containment. Plant Soil, 266, 105-116.

[102]   Vilvert, R.M., Aguiar, D., Gimenes, T.R.M. and Alberton, O. (2014) Residual Effect of Transgenic Soybean in Soil Microbiota. African Journal of Agricultural Research, 9, 2369-2376.

[103]   Lagos, L., Maruyama, F., Nannipieri, P., Mora, M.L., Ogram, A. and Jorquera, M.A. (2015) Current Overview on the Study of Bacteria in the Rhizosphere by Modern Molecular Techniques, a Mini-Review. Journal of Soil Science and Plant Nutrition, 15, 504-523.

[104]   Souza, R.C., Cantãoc, M.E., Ribeiro Vasconcelos, A.M., Nogueira, M.A. and Hungri M. (2013) Soil Metagenomics Reveals Differences under Conventional and No-Tillage with Crop Rotation or Succession. Applied Soil Ecology, 72, 49-61.

[105]   Fierer, N., Lauber, C.L., Ramirez, K.S., Zaneveld, J., Bradford, M.A. and Knight, R. (2012) Comparative Metagenomic, Phylogenetic and Physiological Analyses of Soil Microbial Communities Across Nitrogen Gradients. The ISME Journal, 6, 1007-1017.

[106]   Carbonetto, B., Rascovan, N., álvarez, R., Mentaberry, A. and Vázquez, M.P. (2014) Structure, Composition and Metagenomic Profile of Soil Microbiomes Associated to Agricultural Land Use and Tillage Systems in Argentine Pampas. PloS ONE, 9, e99949.