The use of manure shifts the response of α-diversity and network while not β-diversity of soil microbes to altered irrigation regimes

In irrigation-fed agriculture, both irrigation and fertilization are important management practices. The effects of altering irrigation regimes, fertilization types and their interaction on the soil microbes are unclear. Based on long-term irrigation regimes × fertilization interaction field experiments, soil respiration, the α- and β-diversity, and the community networks were investigated. Under chemical fertilization, reducing irrigation consistently decreased soil respiration and microbial biomass N contents, as well the Chao1 and Shannon indices of bacteria, while increased the Chao1 and Shannon indices of fungi. The manure had a significant interaction with irrigation regimes on organic carbon, total nitrogen, and microbial nitrogen, as well as the Chao1, Shannon, and Simpson indices in both bacteria and fungi. The β-diversities of bacteria and fungi were unchanged by irrigation and fertilization. The soil properties, i.e., water content, organic carbon, pH, total nitrogen, and available P, governed the bacterial community structure independent of fertilization. For fungal community structure, compared with only the significant effect of water content under chemical fertilizer, the use of manure showed an effect by changing numerous soil properties, especially organic carbon and total nitrogen. For microbial network, manure significantly enhanced the positive links of bacterial keystone taxa but not of fungi. As the predominant bacteria and fungi, the abundance of Acidobacteria and Ciliophora was significantly reduced following reduced irrigation, irrespective of fertilization. The abundances of Bacteroidetes, Proteobacteria, and Ascomycota were enhanced following reduced irrigation, while not apparent with manure. Soil respiration, as a key ecological function, had significant relations with chao1 index of bacteria and fungi, while not with β-diversity. In synthesis, this study found that the manure showed a clear buffer effect on the perturbation of reduced irrigation on α-diversity of bacteria. However, the irrigation and manure did not impact on β-diversities of bacteria and fungi. They keystone taxa of microbes and their network have been dramatically altered by manure at the phylum level.