Vegetable Productivity, Soil Physicochemical and Biochemical Properties, and Microbiome in Response to Organic Substitution in an Intensive Greenhouse Production System

Partial substitution of mineral N fertilizer with manure (organic substitution) is considered as an effective way to reduce N input in intensive agroecosystems. Here, based on a 3-year field experiment, we assessed the influence of different organic substitution ratios (15%, 30%, 45%, and 60%, composted chicken manure applied) on vegetable productivity and soil physicochemical and biochemical properties as well as microbiome (metagenomic sequencing) in an intensive greenhouse production system (cucumber-tomato rotation). Organic substitution ratio in 30% got a balance between stable vegetable productivity and maximum N reduction. However, higher substitution ratios decreased annual vegetable yield by 23.29–32.81%. Organic substitution (15–45%) improved soil fertility (12.18–19.94% increase in soil total organic carbon content) and such improvement was not obtained by higher substitution ratio. Soil mean enzyme activity was stable to organic substitution despite the activities of some selected enzymes changed (catalase, urease, sucrase, and alkaline phosphatase). Organic substitution changed the species and functional structures rather than diversity of soil microbiome, and enriched the genes related to soil denitrification (including nirK , nirS , and nosZ ). Besides, the 30% of organic substitution obviously enhanced soil microbial network complexity and this enhancement was mainly associated with altered soil pH. At the level tested herein, organic substitution ratio in 30% was suitable for greenhouse vegetable production locally. Long-term influence of different organic substitution ratios on vegetable productivity and soil properties in intensive greenhouse system needs to be monitored.