Clay-to-Carbon Ratio Controls the Effect of Herbicide Application on Soil Bacterial Richness and Diversity in a Loamy Field

  • H. M. L. I. Herath
  • Per Moldrup
  • Lis W. de Jonge
  • Mogens Nicolaisen
  • Trine Norgaard
  • Emmanuel Arthur
  • Marcos ParadeloEmail author


Soil texture and soil organic carbon (OC) influence the bacterial microenvironment and also control herbicide sorption. A field-scale exploratory study was conducted to investigate the potential interaction between soil texture parameters, herbicides, and soil bacterial richness and diversity. Glyphosate and bentazon were used to evaluate the herbicidal effect on bacterial community under different conditions created by clay and OC gradients in a loamy field. Metabarcoding by high-throughput sequencing of bacterial rDNA was used to estimate bacterial richness and diversity using OTUs, abundance-based coverage (ACE), Shannon diversity index, and phylogenetic diversity. In general, bacterial richness and diversity increased after bentazon application and decreased after glyphosate application. There was no significant effect for field locations with Dexter n (the ratio between clay and OC) values below 4.04 (the median of the values in the field study). The correlation coefficient (r) between bacterial richness and clay decreased after bentazon application, but increased after glyphosate application. Correlations between Dexter n and bacterial indices followed the same pattern, decreasing after bentazon application and increasing after glyphosate application. This indicated that the specific chemical nature of individual herbicides affected bacterial communities. This study reinforced the importance of including soil physical and chemical characteristics to explain the influence of pesticides on the variation in soil bacterial communities in agroecosystems.


Bentazon Glyphosate ACE Shannon Soil texture Metabarcoding 



The technical assistance of Stig T. Rasmussen, Bodil B. Christensen, Jørgen M. Nielsen, Michael Koppelgaard and Janne H. Hansen are gratefully acknowledged. The study was part of the Soil Infrastructure, Interfaces, and Translocation Processes in Inner Space (Soil-it-is) project, which is funded by the Danish Research Council for Technology and Production Science.


  1. Allegrini, M., Zabaloy, M. C., & Gomez, E. D. (2015). Ecotoxicological assessment of soil microbial community tolerance to glyphosate. Science of the Total Environment, 533, 60–68.CrossRefGoogle Scholar
  2. Allievi, L., Gigliotti, C., Salardi, C., Valsecchi, G., Brusa, T., & Ferrari, A. (1996). Influence of the herbicide bentazon on soil microbial community. Microbiological Research, 151, 105–111.CrossRefGoogle Scholar
  3. Bach, E. M., Baer, S. G., Meyer, C. K., & Six, J. (2010). Soil texture affects soil microbial and structural recovery during grassland restoration. Soil Biology and Biochemistry, 42, 2182–2191.CrossRefGoogle Scholar
  4. Banks, M. L., Kennedy, A. C., Krerner, R. J., & Eivazi, F. (2014). Soil microbial community response to surfactants and herbicides in two soils. Applied Soil Ecology, 74, 12–20.CrossRefGoogle Scholar
  5. Borggaard, O. K., & Gimsing, A. L. (2008). Fate of glyphosate in soil and the possibility of leaching to ground and surface waters: a review. Pest Management Science, 64, 441–456.CrossRefGoogle Scholar
  6. Caporaso, J. G., Bittinger, K., Bushman, F. D., Desantis, T. Z., Andersen, G. L., & Knight, R. (2010a). Pynast: a flexible tool for aligning sequences to a template alignment. Bioinformatics, 26, 266–267.CrossRefGoogle Scholar
  7. Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Pena, A. G., Goodrich, J. K., Gordon, J. I., Huttley, G. A., Kelley, S. T., Knights, D., Koenig, J. E., Ley, R. E., Lozupone, C. A., Mcdonald, D., Muegge, B. D., Pirrung, M., Reeder, J., Sevinsky, J. R., Tumbaugh, P. J., Walters, W. A., Widmann, J., Yatsunenko, T., Zaneveld, J., & Knight, R. (2010b). QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7, 335–336.CrossRefGoogle Scholar
  8. Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C. A., Turnbaugh, P. J., Fierer, N., & Knight, R. (2011). Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences of the United States of America, 108, 4516–4522.CrossRefGoogle Scholar
  9. Chazdon, R.L., Colwell, R.K., Denslow, J.S., & Guariguata, M. R. D. O. E. A. E. B., University Of Connecticut, Storrs, Connecticut 06269 (USA) (1998). Statistical methods for estimating species richness of woody regeneration in primary and secondary rain forests of Northeastern Costa Rica.Google Scholar
  10. Constancias, F., Terrat, S., Saby, N. P. A., Horrigue, W., Villerd, J., Guillemin, J.-P., Biju-Duval, L., Nowak, V., Dequiedt, S., Ranjard, L., & Chemidlin Prévost-Bouré, N. (2015). Mapping and determinism of soil microbial community distribution across an agricultural landscape. MicrobiologyOpen, 4, 505–517.CrossRefGoogle Scholar
  11. Cycoń, M., Markowicz, A., & Piotrowska-Seget, Z. (2013a). Structural and functional diversity of bacterial community in soil treated with the herbicide napropamide estimated by the DGGE, CLPP and r/K-strategy approaches. Applied Soil Ecology, 72, 242–250.CrossRefGoogle Scholar
  12. Cycoń, M., Piotrowska-Seget, Z., & Kozdrój, J. (2010). Linuron effects on microbiological characteristics of sandy soils as determined in a pot study. Annals of Microbiology, 60, 439–449.CrossRefGoogle Scholar
  13. Cycoń, M., Wójcik, M., Borymski, S., & Piotrowska-Seget, Z. (2013b). Short-term effects of the herbicide napropamide on the activity and structure of the soil microbial community assessed by the multi-approach analysis. Applied Soil Ecology, 66, 8–18.CrossRefGoogle Scholar
  14. De Jonge, H., De Jonge, L. W., & Jacobsen, O. H. (2000). [C-14] glyphosate transport in undisturbed topsoil columns. Pest Management Science, 56, 909–915.CrossRefGoogle Scholar
  15. De Jonge, L. W., Moldrup, P., & Schjonning, P. (2009). Soil infrastructure, interfaces & translocation processes in inner space (“Soil-it-is”): towards a road map for the constraints and crossroads of soil architecture and biophysical processes. Hydrology and Earth System Sciences, 13, 1485–1502.CrossRefGoogle Scholar
  16. Dequiedt, S., Saby, N. P. A., Lelievre, M., Jolivet, C., Thioulouse, J., Toutain, B., Arrouays, D., Bispo, A., Lemanceau, P., & Ranjard, L. (2011). Biogeographical patterns of soil molecular microbial biomass as influenced by soil characteristics and management. Global Ecology and Biogeography, 20, 641–652.CrossRefGoogle Scholar
  17. Desantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology, 72, 5069–5072.CrossRefGoogle Scholar
  18. Dexter, A. R., Richard, G., Arrouays, D., Czyz, E. A., Jolivet, C., & Duval, O. (2008). Complexed organic matter controls soil physical properties. Geoderma, 144, 620–627.CrossRefGoogle Scholar
  19. Duke, S. O., & Powles, S. B. (2008). Glyphosate: a once-in-a-century herbicide. Pest Management Science, 64, 319–325.Google Scholar
  20. Faith, D. P. (1992). Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1–10.CrossRefGoogle Scholar
  21. Gaston, L. A., Locke, M. A., Wagner, S. C., Zablotowicz, R. M., & Reddy, K. N. (1996). Sorption of bentazon and degradation products in two Mississippi soils. Weed Science, 44, 678–682.Google Scholar
  22. Gee, G.W., & Or, D. (2002). Particle-size analysis. In J. H. Dane & G.C. Topp (Eds.), Methods of soil analysis. Part 4. SSSA Book Series No. 5 (pp. 255–293). Madison, WI: SSSA.Google Scholar
  23. Ghafoor, A., Jarvis, N. J., & Stenstrom, J. (2013). Modelling pesticide sorption in the surface and subsurface soils of an agricultural catchment. Pest Management Science, 69, 919–929.CrossRefGoogle Scholar
  24. Hajibabaei, M., Shokralla, S., Zhou, X., Singer, G.A.C., & Baird, D.J. (2011). Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE, 6.Google Scholar
  25. Hu, H. W., Zhang, L. M., Yuan, C. L., & He, J. Z. (2013). Contrasting euryarchaeota communities between upland and paddy soils exhibited similar pH-impacted biogeographic patterns. Soil Biology and Biochemistry, 64, 18–27.CrossRefGoogle Scholar
  26. Huber, R., & Otto, S. (1994). Environmental behavior of bentazon herbicide. Reviews of Environmental Contamination and Toxicology, 137, 111–134.Google Scholar
  27. Haas, B. J., Gevers, D., Earl, A. M., Feldgarden, M., Ward, D. V., Giannoukos, G., Ciulla, D., Tabbaa, D., Highlander, S. K., Sodergren, E., Methe, B., Desantis, T. Z., Petrosino, J. F., Knight, R., Birren, B. W., & Consortium, H. M. (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Research, 21, 494–504.CrossRefGoogle Scholar
  28. Jacobsen, C. S., & Hjelmsø, M. H. (2014). Agricultural soils, pesticides and microbial diversity. Current Opinion in Biotechnology, 27, 15–20.CrossRefGoogle Scholar
  29. Jarvis, N. J. (2007). A review of non-equilibrium water flow and solute transport in soil macropores: principles, controlling factors and consequences for water quality. European Journal of Soil Science, 58, 523–546.CrossRefGoogle Scholar
  30. Keller, T., & Dexter, A. R. (2012). Plastic limits of agricultural soils as functions of soil texture and organic matter content. Soil Research, 50, 7–17.CrossRefGoogle Scholar
  31. Lancaster, S. H., Hollister, E. B., Senseman, S. A., & Gentry, T. J. (2010). Effects of repeated glyphosate applications on soil microbial community composition and the mineralization of glyphosate. Pest Management Science, 66, 59–64.CrossRefGoogle Scholar
  32. Lane, M., Lorenz, N., Saxena, J., Ramsier, C., & Dick, R. P. (2012). The effect of glyphosate on soil microbial activity, microbial community structure, and soil potassium. Pedobiologia, 55, 335–342.CrossRefGoogle Scholar
  33. Lauber, C. L., Hamady, M., Knight, R. & 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.Google Scholar
  34. Lindhardt, B., Abildtrup, C., Vosgerau, H., Olsen, P., Torp, S., Iversen, B.V., Jørgensen, J.O., Plauborg, F., Rasmussen, P., & Gravesen, P. (2001). The Danish pesticide leaching assessment programme: site characterization and monitoring design. Copenhagen, Denmark: Geological Survey of Denmark and Greenland.Google Scholar
  35. Lo, C. C. (2010). Effect of pesticides on soil microbial community. Journal of Environmental Science and Health, Part B: Pesticides, Food Contaminants, and Agricultural Wastes, 45, 348–359.CrossRefGoogle Scholar
  36. Lupwayi, N. Z., Harker, K. N., Clayton, G. W., Turkington, T. K., Rice, W. A., & O’Donovan, J. T. (2004). Soil microbial biomass and diversity after herbicide application. Canadian Journal of Plant Science, 84, 677–685.CrossRefGoogle Scholar
  37. Maclean, D., Jones, J. D. G., & Studholme, D. J. (2009). Application of ‘next-generation’ sequencing technologies to microbial genetics. Nature Reviews Microbiology, 7, 287–296.Google Scholar
  38. Mahia, J., Gonzalez-Prieto, S. J., Martin, A., Baath, E., & Diaz-Ravina, M. (2011). Biochemical properties and microbial community structure of five different soils after atrazine addition. Biology and Fertility of Soils, 47, 577–589.CrossRefGoogle Scholar
  39. Marsh, J. A. P., Wingfield, G. I., Da Vies, H. A., & Grossbard, E. (1978). Simultaneous assessment of various responses of the soil microflora to bentazone. Weed Research, 18, 293–300.CrossRefGoogle Scholar
  40. Naveed, M., Herath, L., Moldrup, P., Arthur, E., Nicolaisen, M., Norgaard, T., Ferré, T. P. A., & De Jonge, L. W. (2016). Spatial variability of microbial richness and diversity and relationships with soil organic carbon, texture and structure across an agricultural field. Applied Soil Ecology, 103, 44–55.CrossRefGoogle Scholar
  41. Poly, F., Ranjard, L., Nazaret, S., Gourbière, F., & Monrozier, L. J. (2001). Comparison of nifH gene pools in soils and soil microenvironments with contrasting properties. Applied and Environmental Microbiology, 67, 2255–2262.CrossRefGoogle Scholar
  42. Price, M.N., Dehal, P.S., & Arkin, A.P. (2010). Fasttree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE, 5.Google Scholar
  43. Quince, C., Lanzen, A., Davenport, R.J., & Turnbaugh, P.J. (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics, 12.Google Scholar
  44. Ranjard, L., Poly, F., Combrisson, J., Richaume, A., Gourbiere, F., Thioulouse, J., & Nazaret, S. (2000). Heterogeneous cell density and genetic structure of bacterial pools associated with various soil microenvironments as determined by enumeration and DNA fingerprinting approach (RISA). Microbial Ecology, 39, 263–272.Google Scholar
  45. Ranjard, L., & Richaume, A. (2001). Quantitative and qualitative microscale distribution of bacteria in soil. Research in Microbiology, 152, 707–716.CrossRefGoogle Scholar
  46. Ratcliff, A. W., Busse, M. D., & Shestak, C. J. (2006). Changes in microbial community structure following herbicide (glyphosate) additions to forest soils. Applied Soil Ecology, 34, 114–124.CrossRefGoogle Scholar
  47. Schjonning, P., De Jonge, L.W., Munkholm, L.J., Moldrup, P., Christensen, B.T., & Olesen, J.E. (2012). Clay dispersibility and soil friability-testing the soil clay-to-carbon saturation concept. Vadose Zone Journal, 11.Google Scholar
  48. Seghers, D., Verthé, K., Reheul, D., Bulcke, R., Siciliano, S. D., Verstraete, W., & Top, E. M. (2003). Effect of long-term herbicide applications on the bacterial community structure and function in an agricultural soil. FEMS Microbiology Ecology, 46, 139–146.CrossRefGoogle Scholar
  49. Shannon, C. E. (1948). A mathematical theory of communication. Bell System Technical Journal, 27, 379–423.CrossRefGoogle Scholar
  50. Sihtmäe, M., Blinova, I., Künnis-Beres, K., Kanarbik, L., Heinlaan, M., & Kahru, A. (2013). Ecotoxicological effects of different glyphosate formulations. Applied Soil Ecology, 72, 215–224.CrossRefGoogle Scholar
  51. Soares, A., Paradelo, M., Moldrup, P., Delerue-Matos, C., & De Jonge, L. (2015). Predictivity strength of the spatial variability of phenanthrene sorption across two sandy loam fields. Water, Air, & Soil Pollution, 226, 1–13.CrossRefGoogle Scholar
  52. Soares, A.A., Moldrup, P., Minh, L.N., Vendelboe, A.L., Schjonning, P., & De Jonge, L.W. (2013). Sorption of phenanthrene on agricultural soils. Water Air, and Soil Pollution, 224.Google Scholar
  53. Thorstensen, C. W., Lode, O., Eklo, O. M., & Christiansen, A. (2001). Sorption of bentazone, dichlorprop, MCPA, and propiconazole in reference soils from Norway. Journal of Environmental Quality, 30, 2046–2052.CrossRefGoogle Scholar
  54. Vinther, F. P., Eiland, F., Lind, A. M., & Elsgaard, L. (1999). Microbial biomass and numbers of denitrifiers related to macropore channels in agricultural and forest soils. Soil Biology and Biochemistry, 31, 603–611.CrossRefGoogle Scholar
  55. Weiss, A., & Hays, C. J. (2005). Calculating daily mean air temperatures by different methods: implications from a non-linear algorithm. Agricultural and Forest Meteorology, 128, 57–65.CrossRefGoogle Scholar
  56. Zabaloy, M. C., Garland, J. L., & Gomez, M. A. (2008). An integrated approach, to evaluate the impacts of the herbicides glyphosate, 2,4-D and metsulfuron-methyl on soil microbial communities in the Pampas Region, Argentina. Applied Soil Ecology, 40, 1–12.CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.Department of AgroecologyAarhus UniversityTjeleDenmark
  2. 2.Department of Civil EngineeringAalborg UniversityAalborg EDenmark
  3. 3.Department of AgroecologyAarhus UniversitySlagelseDenmark
  4. 4.Soil Science Group, Department of Plant Biology and Soil Science, Faculty of SciencesUniversity of VigoOurenseSpain

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