This study showed that soil biodiversity, especially bacterial diversity, declines with 30 years of citrus planting, and this decline is associated with soil acidification (Fig. S1). It was also found that specific managements that increase soil pH, such as wheat straw addition, can alleviate the negative impact of crop plantation on soil biodiversity. We also found that the effect of citrus planting on the C cycle was different from that on N and P cycle. Citrus planting promoted the N and P cycle but reduced the C cycle, which was indirectly driven by reduction in soil biodiversity. Together, these findings indicate the importance of maintaining the soil biodiversity and functions in orchard cultivation, and demonstrate some effective management practices to reduce the negative impacts.
Citrus Planting Reduces Soil Microbial Communities
Conversion from natural to agricultural ecosystems has been considered as the most important driving force to regulate soil microbial communities (37). In this study, citrus planting was found to reduce soil bacterial and fungal diversity in a time dependent manner. Similarly, Berkelmann et al. (2020) found that the conversion from rainforest to rubber and oil palm plantation resulted in a decline in bacterial diversity. These negative effects of the conversion of natural vegetation land to agricultural land on soil bacterial diversity may be ascribed to the homogenization of soil bacteria (38). In an agriculatural ecosystem, the application of organic or inorganic fertilizers would decrease the local bacterial diversity. On the contrary, conversion of tropical forest to agriculture land improved the soil bacterial diversity through an increase in soil pH (39). In our study, citrus planting caused a decline in soil pH, resulting in decreases in soil bacterial diversity. Soil pH has been widely accepted as the most important factor that affects soil bacterial/fungal community composition (Lauber et al., 2009; Rousk et al., 2010; Zeng et al., 2019a; Zeng et al., 2016).
The conversion of natural vegetation land to citrus orchards altered the soil microbial community composition, which is in agreement with the results in previous studies (37). Proteobacteria (Alphaproteobacteria and Deltaproteobacteria) and Acidobacteria (Subgroup_6 and Subgroup_4) were negatively influenced by the conversion, which might be due to the decline in soil pH and SOC. The dramatic increase in soil Actinobacteria indicates its important role in citrus planting soils, because it has been reported that deforested soils has a low abundance Actinobacteria (40). Considering the sharp loss of plant diversity in the agricultural ecosystem, the reduction of soil bacterial communities might be ascribed to the decreases in plant-related microbial groups, such as mycorrhizal fungi and rhizosphere microbes (41). For example, Rhizobiales are highly related to the diversity of aboveground plants, and thus a decrease in plant diversity would lead to corresponding decreases in Rhizobiales (37, 42).
Cover cropping has been considered as a promising agricultural practice to improve soil quality, enhance crop yields, and increase soil microbial abundance and diversity (43–45). In this study, we found that the application of wheat straw on the soil surface could enhance the SOC, TN, pH and other properties, which might directly or indirectly increase soil microbial diversity and abundance. These positive effects of straw covering on the composition and diversity of soil microbial community are in line with previous studies (46, 47). One possible reason is that the long-term application of straw could relieve soil acidification, which would directly influence the composition of soil bacterial/fungal community. The increase in soil pH due to straw covering enhanced the soil bacterial Shannon index from 10.1 to 10.7 compared with no straw covering within the same planting years (15 years). Similarly, Bu et al. (2020) also repored positive effects of straw returning on the soil bacterial Shannon diversity, which might be attributed to increases in soil organic matter. Therefore, changes in SOC and pH together can explain the variations in soil bacterial diversity under the application of straw in this study.
Citrus Planting Reduces Soil Ecosystem Multifunctionality
The composition and diversity of soil microbial community play central roles in ecosystem multifunctionality in drylands and long-term fertilized soils (23–25). Here, our results suggest that citrus planting significantly alters ecosystem multifunctionality, confirming that land use types have significant impacts on soil ecological functions (48). Compared with natural vegetation, citrus planting increased NEMF and PEMF but reduced CEMF, while the application of wheat straw could enhance the CEMF, implying that the application of straw may alleviate some negative effects of highly intensive citrus planting, such as soil acidification and decreases in soil organic matter, nutrients and soil biodiversity. It has been reported that soil biodiversity has great impacts on soil ecological functions. Any loss in soil biodiversity might decline the ecosystem multifunctionality (25). In this aspect, citrus planting reduces the soil multifunctionality, which might be alleviated by straw application.
It seems that not all studies concluded that microbial diversity has a strong effect on soil multifunctionality. Li et al. (2019) reported that it is fungal richness but not bacterial richness that contributes to multifunctionality in boreal forest soils. In the present study, we also found that soil fungal Shannon diversity explained more variations in NEMF and PEMF than bacterial Shannon diversity. The association between soil bacterial diversity and NEMF was not significant, suggesting that fungi play a dominant role in controlling NEMF. However, fungal communities contributed less to soil multifunctionality (CEMF, NEMF and PEMF) than bacterial communities. Most bacterial phyla have been identified as important predictors of soil multifunctionality by Random Forest regression and Pearson correlation analysis. These dominant bacterial phyla participate in the main soil processes related to multiple functions such as C, N and P cycle. For example, members of Patescibacteria, Deinococcus.Thermus, Cyanobacteria and Actinobacteria reduced soil CEMF, while members of Acidobacteria, Chloroflexi and Planctomycetes improved soil CEMF. Fungi mainly affected NEMF, as confirmed by the association between NEMF and the relative abundance of Basidiomycota and Ascomycota. CEMF and NEMF are mainly associated with soil bacterial phyla. These positive or negative associations of bacterial taxa with soil multifunctionality might be ascribed to their life strategies and ecological functions. Citrus planting would alter these main dominant phyla (Fig. S2), leading to variations of soil multifunctionality. These results demonstrate that soil bacterial community composition and diversity largely determine soil multifunctionality in highly intensive citrus planting ecosystem.
Cover cropping is known as an effective way to enhance soil quality. In this study, cover cropping with peanut had significant effects on CEMF and PEMF; while the application of wheat straw improved CEMF. Both methods of surface covering had no significant effects on NEMF. The application of straw would improve the diversity and abundance of microbes that degrade organic matter. Straw decomposition has been considered as an important source of soil organic matter and nutrients, which has indirect impacts on the growth and production of microbes. The higher bacterial and fungal diversity and CEMF in 15y-SM confirmed that long-term application of straw has positive effects on soil biodiversity and multifunctionality. Surface covering with peanut reduced soil biodiversity, but increased soil PEMF.
Citrus Planting Alters Ecological Clusters Of Soil Microbes
Our results suggest that the conversion of natural vegetation land to agricultural land alters the ecological clusters of soil bacteria and fungi. For example, citrus planting mainly affected ecological cluster #1 and #2, while had little effect on cluster #0, which was dominant in natural vegetation land. Soil Rhizobiales were mainly distributed in ecological cluster #0, due to the higher plant diversity on natural vegetation land than on agricultural land (37). Similarly, higher abundance of soil Rhizobiales was observed in the forest sites (49). In this study, most members of cluster #0 preferred a higher soil pH, confirming that soil pH mediates soil microbial community composition in forests (50). The significant association between the diversity of cluster #0 and CEMF suggests that the main ecological function of cluster #0 is related to soil C cycle. Ecological cluster #1 and #2 are mainly related to NEMF, including a large number of Burkholderia, which are main N fixers in soils (2). Soil Burkholderia prefers to utilize the available N in the soil rather than N fixation (51), and is more abundant in agricultural soils. Burkholderia belongs to Alphaproteobacteria, which are widely distributed in nutrient-rich soils as a life strategy (copiotrophs) (51). The application of fertilizers for citrus planting may stimulate the growth of these copiotrophic bacteria and enhance their abundance. The significant association between the diversity of cluster #1 and #2 and NEMF confirms their ecological functions related N cycles.