Abstract
The soil environment determines plants’ health and performance during their life cycle. Therefore, ecological understanding on variations in soil environments, including physical, chemical, and biological properties, is crucial for managing agricultural fields. Here, we present a comprehensive and extensive blueprint of the bacterial, archaeal, and fungal communities in rice paddy soils with differing soil types and chemical properties. We discovered that natural variations of soil nutrients are important factors shaping microbial diversity. The responses of microbial diversity to soil nutrients were related to the distribution of microbial trophic lifestyles (oligotrophy and copiotrophy) in each community. The compositional changes of bacterial and archaeal communities in response to soil nutrients were mainly governed by oligotrophs, whereas copiotrophs were mainly involved in fungal compositional changes. Compositional shift of microbial communities by fertilization is linked to switching of microbial trophic lifestyles. Random forest models demonstrated that depletion of prokaryotic oligotrophs and enrichment of fungal copiotrophs are the dominant responses to fertilization in low-nutrient conditions, whereas enrichment of putative copiotrophs was important in high-nutrient conditions. Network inference also revealed that trophic lifestyle switching appertains to decreases in intra- and inter-kingdom microbial associations, diminished network connectivity, and switching of hub nodes from oligotrophs to copiotrophs. Our work provides ecological insight into how soil nutrient-driven variations in microbial communities affect soil health in modern agricultural systems.
Highlights
The ongoing rapid increase in the world’s population necessitates improvements in crop productivity
Since we found that soil nutrients (SOM and total nitrogen (TN)) and fertilization significantly influence the diversity of microbial communities, we hypothesized that microbial trophic lifestyles could be related to variations in communities
Methanogenic archaea that can colonize the detected (Supplementary Figure 2B). These results suggest rice root endosphere (Methanobacterium) and rhizosphere that pre-season soils harbor soil microbial communities that can be detected during cropping season, it remains unclear whether these communities are active or dormant
Summary
The ongoing rapid increase in the world’s population necessitates improvements in crop productivity. Crop productivity is determined by the climate, water content, available nutrients, and biological factors. The use of chemical fertilizers and pesticides improves crop productivity by providing sufficient nutrients and protection against insect pests and microbial pathogens. Agrochemicals promote soil degradation by increasing the salinity and acidity of soils and decrease the biodiversity of agricultural environments (Matson, 1997), hampering sustainability. To improve both crop performance and environmental quality, precision agriculture (site-specific crop management) has been proposed (McBratney et al, 2005). Edaphic variables (such as topography, organic matter content, moisture levels, nitrogen levels, and other factors) are measured for intra- and interfield comparisons. Soil microbial communities, key component of soil properties, are infrequently considered among measurable edaphic factors
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call