Abstract
Soil is a complex and dynamic ecosystem whose functionality is related to the equilibrium existing among chemical, physical and biological parameters and the resident microbial communities. Soil microorganisms play a central role in decomposing organic matter, in determining the release of mineral nutrients, and in nutrient cycling, and have direct and indirect effects on both crop growth and quality, as well as on the sustainability of soil productivity. In addition, soil microorganisms substantially contribute to the resistance and resilience of agro-ecosystems to abiotic disturbance and stress. Therefore, changes in microbial communities may directly affect soil ecosystem function since microbes can respond rapidly to environmental changes because of the vastness of microbial biomass and diversity. An increasing number of studies have shown how environmental impacts that cause modifications in microbial community structure and diversity ultimately affect soil biological processes. Agricultural land management is one of most significant anthropogenic activities that substantially alter soil characteristics, including physical, chemical, and biological properties. The present chapter gives a picture of the effect of different agricultural management practices on soil microbial community structure and function. A case study on the effects of tillage and nitrogen fertilization on soil bacterial community structure is also reported.
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References
Acosta-Martínez, V., Zobeck, T. M., & Allen, V. (2004). Soil microbial, chemical and physical properties in continuous cotton and integrated crop–livestock systems. Soil Science Society of America Journal, 68, 1875–1884.
Acosta-Martínez, V., Dowd, S. E., Bell, C. W., Lascano, R., Booker, J. D., Zobeck, T. M. M., & Upchurch, D. R. (2010). Microbial community composition as affected by dryland cropping systems and tillage in a semiarid sandy soil. Diversity, 2, 910–931.
Acosta-Martínez, V., Lascano, R., Calderón, F., Booker, J. D., Zobeck, T. M., & Upchurch, D. R. (2011). Dryland cropping systems influence the microbial biomass and enzyme activities in a semiarid sandy soil. Biology and Fertility of Soils, 47, 655–667.
Aislabie, J., & Deslippe, J. R. (2013). Soil microbes and their contribution to soil services. In J. R. Dymond (Ed.), Ecosystem services in New Zealand – conditions and trends (pp. 143–161). Lincoln: Manaaki Whenua Press.
Allison, S. D., & Martiny, J. B. H. (2008). Resistance, resilience, and redundancy in microbial communities. Proceedings of the National Academy of Sciences, 12, 11512–11519.
Atlas, R. M., Horowitz, A., Krichevsky, M., & Bej, A. K. (1991). Response of microbial populations to environmental disturbance. Microbial Ecology, 22, 249–256.
Bannert, A., Kleineidam, K., Wissing, L., Mueller-Niggemann, C., Vogelsang, V., Welzl, G., Cao, Z., & Schloter, M. (2011). Changes in diversity and functional gene abundances of microbial communities involved in nitrogen fixation, nitrification, and denitrification in a tidal wetland versus paddy soils cultivated for different time periods. Applied Environmental Microbiology, 77, 6109–6116.
Bergsma-Vlami, M., Prins, M. E., & Raaijmakers, J. M. (2005). Influence of plant species on population dynamics, genotypic diversity and antibiotic production in the rhizosphere by indigenous Pseudomonas spp. FEMS Microbiology Ecology, 52, 59–69.
Bevivino, A., Paganin, P., Bacci, G., Florio, A., Sampedro Pellicer, M., et al. (2014). Soil bacterial community response to differences in agricultural management along with seasonal changes in a Mediterranean region. PLoS ONE, 9, e105515.
Bonanomi, G., D'Ascoli, R., Scotti, R., Gaglione, S. A., Caceres, M. G., et al. (2014). Soil quality recovery and crop yield enhancement by combined application of compost and wood to vegetables grown under plastic tunnels. Agriculture Ecosystems and Environment, 192, 1–7.
Botton, S., van Heusden, M., Parsons, J. R., Smidt, H., & van Straalen, N. (2006). Resilience of microbial systems towards disturbances. Critical Review in Microbiology, 32, 101–112.
Buckley, D. H., & Schmidt, T. M. (2003). Diversity and dynamics of microbial communities in soils from agro-ecosystems. Environmental Microbiology, 5, 441–452.
Chaudhry, V., Rehman, A., Mishra, A., Chauhan, P. S., & Nautiyal, C. S. (2012). Organic and chemical amendments changes in bacterial community structure of agricultural land due to long-term organic and chemical amendments. Microbial Ecology, 64, 450–460.
Chiarini, L., Bevivino, A., Dalmastri, C., Nacamulli, C., & Tabacchioni, S. (1998). Influence of plant development, cultivar and soil type on microbial colonization of maize roots. Applied Soil Ecology, 8, 11–18.
Dalmastri, C., Chiarini, L., Cantale, C., Bevivino, A., & Tabacchioni, S. (1999). Soil type and maize cultivar affect the genetic diversity of maize root-associated Burkholderia cepacia populations. Microbial Ecology, 38, 273–284.
De Leij, F. A. A. M., Whipps, J. M., & Lynch, J. M. (1994). The use of colony development for the characterization of bacterial communities in soil and on roots. Microbial Ecology, 27, 81–97.
De Sanctis, G., Roggero, P. P., Seddaiu, G., Orsini, R., Porter, C. H., & Jones, J. W. (2012). Long-term no tillage increased soil organic carbon content of rain-fed cereal systems in a Mediterranean area. European Journal of Agronomy, 40, 18–27.
De Vries, F. T., & Shade, A. (2013). Controls on soil microbial community stability under climate change. Frontiers in Microbiology, 4, 1–16.
Delmont, T. O., Robe, P., Cecillon, S., Clark, I. M., Constancias, F., Simonet, P., Hirsch, P. R., & Vogel, T. M. (2011). Accessing the soil metagenome for studies of microbial diversity. Applied Environmental Microbiology, 77, 1315–1324.
Di Cello, F., Bevivino, A., Chiarini, L., Fani, R., Paffetti, D., & Tabacchioni, S. (1997). Biodiversity of a Burkholderia cepacia population isolated from maize rhizosphere at different plant growth stages. Applied and Environmental Microbiology, 63, 4485–4493.
Dorodnikov, M., Blagodatskaya, E., Blagodatsky, S., Fangmeier, A., & Kuzyakov, Y. (2009). Stimulation of r- vs. K-selected microorganisms by elevated atmospheric CO2 depends on soil aggregate size. FEMS Microbiology Ecology, 69, 43–52.
Dupouey, J. L., Dambrine, E., Laffite, J. D., & Moares, C. (2002). Irreversible impact of past land use on forest soils and biodiversity. Ecology, 83, 2978–2984.
Fierer, N., Leff, J. W., Adams, B. J., Nielsen, U. N., Bates, S. T., et al. (2012). Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proceedings of the National Academy of Sciences, 109, 21390–21395.
Garland, J. L. (1997). Analysis and interpretation of community-level physiological profiles in microbial ecology. FEMS Microbiology Ecology, 24, 289–300.
Ghimire, R., Norton, J. B., Stahl, P. D., & Norton, U. (2014). Soil microbial substrate properties and microbial community responses under irrigated organic and reduced-tillage crop and forage production systems. PLoS ONE, 9, e103901.
Griffiths, B. S., Bonkowski, M., Roy, J., & Ritz, K. (2001). Functional stability, substrate utilization and biological indicators of soils following environmental impacts. Applied Soil Ecology, 16, 49–61.
Hendrix, P. H., Crossley, D. A., & Coleman, D. C. (1990). Soil biota as components of sustainable agro-ecosystem. In C. A. Edwards, R. Lal, P. Madden, R. H. Miller, & G. House (Eds.), Sustainable agricultural systems (pp. 637–654). Soil Water Conservation Society: Iowa.
Hobbs, R. J., & Hueneke, L. F. (1992). Disturbance, diversity, and invasion: Implications for conservation. Conservation Biology, 6, 324–337.
Houghton, R. A., & Goodale, C. (2004). Effects of land-use change on the carbon balance of terrestrial ecosystems. In R. De Fries, G. Asner, & R. A. Houghton (Eds.), Ecosystems and land use change, geophysical monograph series (Vol. 153, pp. 85–98). Washington, DC: American Geophysical Union.
Hugenholtz, P., & Tyson, G. W. (2008). Metagenomics. Nature, 455, 481–484.
Janssen, P. H. (2006). Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Applied and Environmental Microbiology, 72, 1719–1728.
Jurburg, S. D., & Salles, J. F. (2015). Functional redundancy and ecosystem function – The soil microbiota as a case study. In: Y. H. Lo, J. A. Blanco, S. Roy (Eds.), Agricultural and biological sciences. Biodiversity in ecosystems – Linking structure and function (pp. 29–49).
Kirk, J. L., Beaudettea, L. A., Hartb, M., Moutoglisc, P., Klironomos, J. N., Lee, H., & Trevors, J. T. (2004). Methods of studying soil microbial diversity. Journal of Microbiological Methods, 58, 169–188.
Krzyżak, J., Wasilkowski, D., Płaza, G. A., Mrozik, A., Brigmon, R. L., & Pogrzeba, M. (2013). Culture methods as indicators of the biological quality of phytostabilized heavy metal-contaminated soil. Environmental Biotechnology, 9, 6–13.
Lagomarsino, A., Grego, S., Marhan, S., Moscatelli, M. C., & Kandeler, E. (2009). Soil management modifies micro-scale abundance and function of soil microorganisms in a Mediterranean ecosystem. European Journal of Soil Science, 60, 2–12.
Landi, S., Piccolo, R., Simoncini, S., & Pastorelli, R. (2011). Molecular characterization of the microbial community involved in the carbon cycle in different areas and types of soil management. Environmental Quality, 6, 29–38.
Lauber, C. L., Ramirez, K. S., Aanderud, Z., Lennon, J., & Fierer, N. (2013). Temporal variability in soil microbial communities across land-use types. The ISME Journal, 7, 1641–1650.
Levine, U. Y., Teal, T. K., Robertson, G. P., & Schmidt, T. M. (2011). Agriculture’s impact on microbial diversity and associated fluxes of carbon dioxide and methane. The ISME Journal, 5, 1683–1691.
Li, J., Li, Z., Wang, F., Zou, B., Chen, Y., et al. (2015). Effects of nitrogen and phosphorus addition on soil microbial community in a secondary tropical forest of China. Biology and Fertility of Soils, 51, 207–215.
Luo, X., Fu, X., Yang, Y., Cai, P., Peng, S., et al. (2016). Microbial communities play important roles in modulating paddy soil fertility. Nature Scientific Reports, 6, 20326.
Mathew, R. P., Feng, Y., Githinji, L., Ankumah, R., & Balkcom, K. S. (2012). Impact of no-tillage and conventional tillage systems on soil microbial communities. Applied Environmental Soil Sciences, ID 548620. http://dx.doi.org/10.1155/2012/548620.
Michel, H. M., & Williams, M. (2011). Soil habitat and horizon properties impact bacterial diversity and composition. Soil Science Society of America Journal, 75, 1440–1448.
Miller, M., & Dick, R. P. (1995). Thermal stability and activities of soil enzymes influenced by crop rotations. Soil Biology and Biochemistry, 27, 1161–1166.
Myrold, D. D., Zeglin, L. H., & Jansson, J. K. (2014). The potential of metagenomic approaches for understanding soil microbial processes. Soil Science Society of America Journal, 78, 3–10.
Nesme, J., Achouak, W., Agathos, S. N., Bailey, M., Baldrian, P., et al. (2016). Back to the future of soil metagenomics. Frontiers in Microbiology, 7, 1–5.
Nielsen, M. N., & Winding, A. (2002). Microorganisms as indicators of soil health (Technical Report No. 388). National Environmental Research Institute, Denmark. Available at http://www.dmu.dk/1_viden/2_Publikationer/3_fagrapporter/rapporter/FR388.pdf
Øvreås, L. (2000). Population and community level approaches for analyzing microbial diversity in natural environments. Ecology Letters, 3, 236–251.
Pane, C., Piccolo, A., Spaccini, R., Celano, G., Villecco, D., & Zaccardelli, M. (2013). Agricultural waste-based composts exhibiting suppressivity to diseases caused by the phytopathogenic soil-borne fungi Rhizoctonia solani and Sclerotinia minor. Applied Soil Ecology, 65, 43–51.
Papaleo, M. C., Fondi, M., Maida, I., Perrin, E., Bevivino, A., et al. (2015). Analysis of a pool of small plasmids from soil heterotrophic cultivable bacterial communities. The Open Microbiology Journal, 9, 98–109.
Parfitt, R. L., Scott, N. A., Ross, D. J., Salt, G. J., & Tate, K. R. (2003). Land use change effects on soil C and N transformations in soils of high N status: Comparisons under indigenous forest, pasture and pine plantation. Biogeochemistry, 66, 203–221.
Pastorelli, R., Piccolo, R., Cocco, S., & Landi, S. (2010). mRNA recovery and denitrification gene expression in clay-soil bacterial communities under different agricultural managements. Agrochimica, 54, 179–192.
Paula, F. S., Rodrigues, J. L. M., Zhou, J., Wu, L., Mueller, R. C., et al. (2014). Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities. Molecular Ecology, 23, 2988–2999.
Peterson, G., Allen, C. R., & Holling, C. S. (1998). Ecological resilience, biodiversity and scale. Ecosystems, 1, 6–18.
Pianka, E. R. (1970). On r and K selection. The American Naturalist, 104, 592–597.
Preston-Mafham, J., Boddy, L., & Randerson, P. F. (2002). Analysis of microbial, community, functional, diversity, using sole-carbon-source utilisation profiles: a critique. FEMS Microbiology Ecology, 42, 1–14.
Ramachandran, V. K., East, A. K., Karunakaran, R., Downie, J. A., & Poole, P. S. (2011). Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics. Genome Biology, 12, R106–R106.
Rastogi, G., & Sani, R. K. (2011). Molecular techniques to assess microbial community structure, function, and dynamics in the environment. In I. Ahmad, F. Ahmad, & J. Pichtel (Eds.), Microbes and microbial technology: Agricultural and environmental applications (pp. 29–57). New York: Springer.
Sala, O. E., Chapin, F. S., Armesto, J. J., Berlow, E., Bloomfield, J., Dirzo, R., et al. (2000). Biodiversity-global biodiversity scenarios for the year 2100. Science, 287, 1770–1774.
Seddaiu, G., Icola, I., Farina, R., Orsini, R., Iezzi, G., & Roggero, P. P. (2016). Long term effects of tillage practices and N fertilization in rainfed Mediterranean cropping systems: durum wheat, sunflower and maize grain yield. European Journal of Agronomy, 77, 166–178.
Shade, A., Peter, H., Allison, S. D., Baho, D. L., Berga, M., et al. (2012). Fundamentals of microbial community resistance and resilience. Frontiers in Microbiology, 3, 1–19.
Shange, R. S., Ankumah, R. O., Ibekwe, A. M., Zabawa, R., & Dowd, S. E. (2012). Distinct soil bacterial communities revealed under a diversely managed agroecosystem. PLoS ONE, 7, e40338.
Sikorski, J. (2015). The prokaryotic biology of soil. Soil Organisms, 87, 1–28.
Smalla, K., Wieland, G., Buchner, A., Zock, A., Parzy, J., Kaiser, S., & Roskot, N. (2001). Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Applied Environmental Microbiology, 67, 4742–4751.
Staley, J. T., & Konopka, A. (1985). Measurement of in situ activities of non photosynthetic microorganisms in aquatic and terrestrial habitats. Annual Reviews of Microbiology, 39, 321–346.
Stenström, J., Svensson, K., & Johansson, M. (2001). Reversible transition between active and dormant microbial states in soil. FEMS Microbiol Ecology, 36, 93–104.
Tago, K., Ishii, S., Nishizawa, T., Otsuka, S., & Senoo, K. (2011). Phylogenetic and functional diversity of denitrifying bacteria isolated from various rice paddy and rice-soybean rotation fields. Microbes and Environments, 26, 30–35.
Tiedje, J. M., Asuming-Brempong, S., Nusslein, K., Marsh, T. L., & Flynn, S. J. (1999). Opening the black box of soil microbial diversity. Applied Soil Ecology, 13, 109–122.
Tilston, E. L., Sizmur, T., Dixon, G. R., Otten, W., & Harris, J. A. (2010). The impact of land-use practices on soil microbes. In G. R. Dixon & E. L. Tilston (Eds.), Soil microbiology and sustainable crop production (pp. 273–295). New York: Springer.
Torsvik, V., & Øvreås, L. (2002). Microbial diversity and function in soil: from genes to ecosystems. Current Opinion in Microbiology, 5, 240–245.
Van Elsas, J. D., Torsvik, V., Hartmann, A., Øvreås, L., & Jansson, J. K. (2007). The bacteria and archaea in soil. In J. D. Van Elsas, J. K. Jansson, J. T. Trevors (Eds.), Modern soil microbiology (2nd ed, pp. 23–54). Boca Raton: CRC Press.
Vida, C., Bonilla, N., de Vicente, A., & Cazorla, F. M. (2016). Microbial profiling of a suppressiveness-induced agricultural soil amended with composted almond shells. Frontiers in Microbiology, 7, 1–14.
Westergaard, K., Muller, A. K., Christensen, S., Bloem, J., & Sørensen, S. J. (2001). Effects of tylosin as a disturbance on the soil microbial community. Soil Biology and Biochemistry, 33, 2061–2071.
Widenfalk, A., Bertilsson, S., Sundh, I., & Goedkoop, W. (2008). Effects of pesticides on community composition and activity of sediment microbes – Responses at various levels of microbial community organization. Environmental Pollution, 152, 576–584.
Acknowledgements
This study was supported by COST Action FP1305 “BioLink: Linking soil biodiversity and ecosystem function in European forests”. The case-study in the Mediterranean Area was funded by MIUR (Integrated Special Fund for Research– FISR) in the frame of the Italian National Project SOILSINK “Climate change and agro-forestry systems, impacts on soil carbon sink and microbial diversity”, and partially supported by MIUR (Research Department of Italian Government) in the framework of the Agreement Program ENEA-CNR (Art. 2, c. 44, Legge 23.12.2009 n. 191 – Legge Finanziaria 2010). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Authors greatly acknowledge the “Azienda Didattico-Sperimentale Pasquale Rosati” in Agugliano, the coordinator of SOILSINK Project Dr. Rosa Francaviglia (CRA-RPS, Rome), the responsible of the experimental site in Agugliano Prof. Pier Paolo Roggero (University of Sassari), and Dr. Roberto Orsini, Dr. Giuseppe Iezzi and Dr. Giuseppe Corti (Polytechnic University of Marche, Ancona, Italy) for providing data on soil physical properties and collecting soil samples.
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Bevivino, A., Dalmastri, C. (2017). Impact of Agricultural Land Management on Soil Bacterial Community: A Case Study in the Mediterranean Area. In: Lukac, M., Grenni, P., Gamboni, M. (eds) Soil Biological Communities and Ecosystem Resilience. Sustainability in Plant and Crop Protection. Springer, Cham. https://doi.org/10.1007/978-3-319-63336-7_5
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