Soil respiration is a critical process that regulates key ecosystem functions such as climate control, nutrient cycling, and plant productivity. Soil texture, nutrient availability, and microbial communities can all influence soil respiration, yet our understanding of their relative importance remains limited. This study aimed to investigate how different factors—like soil texture, nutrient additions, and microbial communities—contribute to soil respiration and define their specific roles in its variability. Using a microcosm experiment with various fertilizers and two soil types (Navarra, a silty clay soil, and Saponi, a sandy soil), we measured changes in both biotic and abiotic factors. A multiple linear regression analysis revealed that, among other biotic and abiotic factors, soil clay content, soluble nitrogen levels, bacterial abundance, and α-diversity significantly impacted soil respiration, together accounting for over 60% of its total variance. Structural equation modeling indicated that microbial communities made the greatest contribution to respiration at 30.84%, followed by soil texture at 19.63%. Overall, biotic factors were found to play a more significant role in driving soil respiration rates compared to abiotic factors, with edaphic properties having a greater influence than fertilizer additions.

Shotgun metagenomic data analysis for investigating biogeochemical cycles in the environment remains challenging, primarily due to the steep learning curve, intensive time investment, and high computational demands, all of which pose significant barriers for many researchers. We present a new R package called “CNPS.cycle,” designed to streamline the interpretation of shotgun metagenomic data related to biogeochemical processes, complete with visually informative outputs. This comprehensive package comprises four distinct analysis modules, focused on carbon, nitrogen, phosphorus, and sulfur cycling. Users can easily utilize the package by uploading annotation result files derived from shotgun metagenomic data, specifically those based on the Kyoto Encyclopedia of Genes and Genomes and the NCBI non-redundant protein sequence database. The package then automates essential steps, including data preprocessing, curation, and differential analysis of biogeochemical cycle-related genes; analysis of microorganisms possessing biogeochemical cycle-related genes at the contig level; β-diversity analysis; and, finally, data visualization. The outcome is a comprehensive analysis revealing differentially abundant genes and functionally significant microbial entities associated with the carbon, nitrogen, phosphorus, and sulfur cycles, presented in the form of tables and high-quality images. This tool will provide profound insights into the relationship between soil microorganisms and elemental chemical cycles, thereby advancing our comprehension of soil ecosystems. For accessibility, the CNPS.cycle package is available on GitHub ( https://github.com/yuezhengfu/CNPS.cycle ), where detailed instructions on its usage can be found in the project’s GitHub page ( https://github.com/yuezhengfu/CNPS.cycle/wiki ). IMPORTANCE: The “CNPS.cycle” R package offers significant environmental implications by simplifying the analysis of shotgun metagenomic data related to biogeochemical cycles. Its automated workflow identifies key genes and microbes involved in carbon, nitrogen, phosphorus, and sulfur cycling, enhancing our understanding of microbial contributions to ecosystem functions. This tool enables researchers to explore microbial-mediated nutrient cycling more efficiently, supporting informed decisions in environmental management and climate change mitigation. By providing accessible, high-quality outputs, “CNPS.cycle” facilitates data-driven insights into the interplay between microbes and global biogeochemical processes.

Karst desertification causes severe soil erosion, hydrological imbalance, and biodiversity loss, thereby threatening ecosystem resilience and agricultural productivity. Soil carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling underpin ecosystem stability, yet how agricultural management practices regulate multi-element cycling in degraded karst agroecosystems remains poorly understood. Here, we conducted a four-year field trial in a karst mango orchard in southwestern China and integrated metagenomic sequencing with comprehensive soil environmental profiling to investigate how C. rotundifolia cover cropping reshapes soil elemental cycling. Compared with conventional tillage (CK), C. rotundifolia cover cropping (Y) significantly ( p < 0.05) altered topsoil microbial functional profiles and nutrient availability. Carbon cycling potentials, including gene associated with aerobic respiration ( cox1/3 ), fermentation, and CO₂ assimilation—were enriched under C. rotundifolia cover cropping. Nitrogen cycling potentials were enhanced through increased representation of genes involved in denitrification ( nirK/S , nosZ ), nitrogen acquisition, and nitrate reduction ( nirA , narB ), while phosphorus cycling was promoted through enrichment of the PhoR-PhoB phosphate regulatory system. Sulfur transformation potentials were also altered, with increased representation of genes involved in sulfate reduction, oxidation, and sulfonate utilization. Cover cropping substantially improved soil fertility, increasing SOC (+35.4%), NH ₄ ⁺ -N (+31.8%), TN (+35.1%), and AP (+105.9%), while reducing exchangeable Al ³⁺ concentration by 60.9%. Microbial community restructuring was characterized by decreased Actinobacteriota and Chloroflexota and increased Bacteroidota and Proteobacteria, which exhibited central roles in elemental cycling networks. Mantel analyses identified exchangeable Al ³⁺ as a dominant environmental constraint shaping microbial communities involved in C, N, P, and S cycling. Collectively, these findings demonstrate that C. rotundifolia cover cropping enhances karst soil resilience through a coupled microbial-geochemical pathway, in which improved soil chemical conditions and microbial functional reorganization jointly restore elemental cycling capacity.

Soil aggregates, which are highly influenced by land conversion, play key roles in driving soil nutrient distribution and microbial colonization. However, the role of soil aggregates in shaping the responses of microbial community composition and multiple ecosystem functions, especially ecosystem multifunctionality (EMF), to land conversion remains poorly understood. In this study, we investigated the impact of the conversion of a longan orchard (LO) to a conventional tea plantation (CTP) and organic tea plantation (OTP) on soil EMF at the aggregate level and explored the underlying mechanism. Our results showed that EMF was significantly reduced in the conventional tea plantation, with 3.44, 1.79, and 1.24 times for large macro-, macro-, and micro-aggregates. In contrast, it was relatively preserved in the organic tea plantation. Notably, micro-aggregates with higher microbial biomass supported more EMF than larger aggregates under the land conversion conditions. The EMF associated with soil aggregates was found to be regulated by the differences in nutrient content and microbial community composition. Random forest analysis, redundancy analysis, and Pearson analysis indicated that both soil nutrient and microbial community composition within soil aggregates jointly determined EMF. This study highlights that soil aggregation influences the stratification of nutrients and microbial communities, which leads to the differing response of aggregate-related EMF to land conversion.