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Long-term fertilizer and crop-rotation treatments differentially affect soil bacterial community structure

Abstract

Background and aims

Soil microbial communities influence nutrient cycling, chemistry and structure of soil, and plant productivity. In turn, agronomic practices such as fertilization and crop rotation alter soil physical and chemical properties and consequently soil microbiomes. Understanding the long-term effects of agronomic practices on soil microbiomes is essential for improving agronomic practices to optimize these microbial communities for agricultural sustainability. We examine the composition and substrate-utilization profiles of microbial communities at the Morrow Plots in Illinois.

Methods

Microbial community composition is assessed with 16S rRNA gene sequencing and subsequent bioinformatic analyses. Community- level substrate utilization is characterized with the BIOLOG EcoPlate.

Results

Fertilizer and rotation treatments significantly affected microbial community structure, while substrate utilization was affected by fertilizer, but not crop-rotation treatments. Differences in relative abundance and occurrence of bacterial taxa found in fertilizer treatments can explain the observed differences in community level substrate utilization.

Conclusion

Long-term fertilization and crop-rotation treatments affect soil microbial community composition and physiology, specifically through chronic nutrient limitation, long-term influx of microbes and organic matter via manure application, as well as through changes in soil chemistry. Relatively greater abundance of Koribacteraceae and Solibacterales taxa in soils might prove useful as indicators of soil degradation.

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Acknowledgments

We would like to acknowledge Robert Dunker and previous managers and the University of Illinois Agricultural Experiment Station for long-term support and maintenance of the Morrow Plots. This work was also supported by the Cooperative State Research, Education, and Extension Service, US Department of Agriculture, under project number ILLU 875-374. The authors are grateful to students enrolled in the Fall 2009 Microbial Ecology Methods course taught by A. Kent for assistance with sample collection and processing. Chinmay Soman is supported by the National Science Foundation through the Science, Engineering, and Education for Sustainability Post-Doctoral Fellowship, Award # 1314064.

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Correspondence to Angela D. Kent.

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Soman, C., Li, D., Wander, M.M. et al. Long-term fertilizer and crop-rotation treatments differentially affect soil bacterial community structure. Plant Soil 413, 145–159 (2017). https://doi.org/10.1007/s11104-016-3083-y

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Keywords

  • Fertilization
  • Crop-rotation
  • Carbon source utilization patterns
  • Indicator species
  • Microbial community composition
  • 16S ribosomal- RNA gene sequencing