The Response of Soil Microbiome-Driven Carbon-Cycling Functional Potential to Continuous Greenhouse Tomato Cultivation

Long-term continuous cropping commonly reduces the yield and quality of greenhouse vegetables and, at the same time, intensifies soil-borne diseases (termed continuous cropping obstacles, CCOs). This cultivation pattern substantially restricts the sustainable productivity of greenhouse vegetable production systems. Alterations in the diversity and structure of the soil microbiome with increased cropping history are thought to be a crucial mechanism underlying CCOs. However, how the soil microbiome functions in response to continuous cropping of greenhouse vegetables remains incompletely understood. Supporting carbon (C) cycling is one of the most vital functions of the soil microbiome in agroecosystems. Using soil metagenomic sequencing, we assessed the influence of continuous greenhouse tomato cropping (0, 10, 20, and 30 years) on soil microbiome-driven C cycling. The results showed that continuous greenhouse tomato cropping significantly reduced the diversity of microbial C-cycling genes and altered their structure. The total relative abundance of C-cycling genes increased linearly with continuous cropping duration. C fixation and decomposition were the predominant soil C metabolic processes, and their relative abundances generally increased over time. Yet C-fixing and -decomposing pathways responded differently to continuous cropping of greenhouse tomato. PC (participating in the reductive citrate cycle) was identified as a candidate crucial C-fixing gene, and SGA1 (participating in starch degradation) was identified as a candidate crucial C-decomposing gene. Soil phosphorus (P) status (total and available P concentrations) was a powerful regulator of soil microbiome-driven C cycling, and soil C availability played an important role in shaping crucial C-cycling genes. Overall, our results revealed that continuous cropping of greenhouse vegetables significantly influenced soil microbiome-driven C cycling, highlighting that shifts in soil nutrient cycling functions should not be ignored when exploring the mechanisms underlying CCOs. The findings from this study broaden understanding of the mechanisms of CCOs in intensive greenhouse vegetable production systems by offering insight into the functional attributes of the soil microbiome.