The response of soil fauna to the litter decomposition process has received considerable attention, but this effect has not been fully examined in agroforestry systems. A 1-year in situ decomposition experiment was carried out in a pure ginkgo plantation and two ginkgo agroforestry systems using a litterbag method (11 different treatments were tested in three systems). We found that the application of different organic materials (crop residues) produced positive effects on the number of soil fauna in the ginkgo planting systems; the mixture of ginkgo leaves and corn leaves was the best performing treatment. Collembola and Acarina were the predominant groups in the litter bags and were mainly responsible for the differences among the treatments. Litter mixing promoted the abundance, richness, and diversity of soil fauna, and significant differences regarding the Shannon–Wiener index of the soil fauna were observed among the 11 treatments in July. Significantly higher soil MBC (microbial biomass carbon) and MBN (microbial biomass nitrogen) were observed in agroforestry systems than in pure ginkgo plantations. These results suggest that the practice of intercrop residue application plays an important role in enhancing soil ecosystem function in ginkgo agroforestry systems and may ultimately contribute to sustainable intercrop production, soil fertility, and local economic diversity.
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