The soil quality index (SQI) is based on several key indicators and is used to assess soil quality. More than 250,000 ha of walnut saplings (
Juglans regia L.) were planted in previous cropland areas in the Sichuan Basin, China, using a range of soil cover types that may affect soil quality with effects that are unclear. We investigated the effects of white film (WF), black film (BF), shade netting (SN), and maize straw (MS) soil cover types and an uncovered control type (CK) on soil chemical and biological indicators and the SQI in the 0–15 cm soil layer in a young walnut forest in the Sichuan Basin over a 27-month study period. The results showed that all soil cover types increased the soil organic matter (SOM), total potassium (TK), and available potassium (AK) concentrations (
p < 0.05), whereas the total nitrogen (TN) and available nitrogen (AN) concentrations were greater only in soils covered by MS than in CK (
p < 0.05). The available phosphorus concentrations were 64.1 and 193.2% greater in soils covered by BF and MS treatments, respectively, than in the CK (
p < 0.05). The numbers of soil faunal groups (
N) were 45.7, 36.4, 37.2, and 101.5% higher in WF, BF, SN, and MS, respectively, than in CK (
p < 0.05); the individual numbers (
S) were 92.3, 36.2, 100.8, and 154.5% greater in WF, BF, SN, and MS, respectively, than in CK (
p < 0.05). The microbial biomass carbon (MBC) was 15.5, 32.3, 45.0, and 77.1% greater in WF, BF, SN, and MS than in CK, respectively (
p < 0.05). Redundancy discriminant analysis revealed strong positive interactions between biological indicators (MBC,
N, and
S) and SOM, AN, and AK concentrations. SOM, TN, AK,
S, and MBC were the minimum required variables for the effective assessment of the SQI. All four soil cover types led to an improved SQI (
p < 0.05), and MS had the greatest effect on SOM, TN, AN, AP,
N,
S, MBC, and SQI (
p < 0.05). In conclusion, all four soil cover types increased the SOM levels, TK, AK, and MBC concentrations, soil faunal diversity, and SQI. The MS treatment was the most cost-effective and efficient measure to improve soil fertility, ecological function, and overall soil quality in the studied walnut forest.
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