Response of the soil microbial community to different fertilizer inputs in a wheat-maize rotation on a calcareous soil

Abstract

The combined use of inorganic fertilizers with organic manures has recently attracted increasing interest in China in attempts to mitigate the deleterious environmental impacts of excessive rates of chemical fertilizers in agroecosystems. However, questions remain concerning temporal change and how the soil microbiome responds to different fertilizer inputs in intensively managed crop rotations. Here, we collected soil samples from a wheat–maize system to investigate the response of the soil microbiome to four years of application of inorganic fertilizer only (NPK), NPK plus either cattle manure or straw, NPK plus both manure and straw, or a zero fertilizer control. The soil bacterial and fungal populations and community composition, nitrogen functional genes (amoA) and carbon utilization patterns were assessed. Sampling time had a much greater influence on the soil microbiome than did fertilizer regime, and the effect of fertilization was mostly significant at the wheat harvest. Fertilization increased amoA gene copy numbers but only AOB abundance showed differences among fertilizer treatments. In June the community composition of both bacteria and fungi was clearly separated between the organic matter additions and the zero organic matter treatments. Microbial carbon source utilization was significantly affected by fertilization regime and sampling time. By contrast, at the maize harvest neither microbial populations nor microbial community composition were altered. Our results suggest that the entire soil microbiome is more responsive to organic inputs than to chemical fertilizers in the short term. Temporal shifts in microbial community composition in the crop rotation imply that crop species and environmental conditions need to be carefully integrated into nutrient management strategies.