Soil microbial community characteristics in greenhouse vegetable production under different fertilization patterns based on metagenomic analysis

Objectives Using metagenomic sequencing technology, we investigated the influence of fertilization patterns on community structure and composition of bacteria, fungi and archaea for sustainable soil health and greenhouse vegetable production.

Methods We conducted a long-term fertilization experiment in a vegetable greenhouse in Tianjin City. The cropping system in this study was spring tomato and autumn-winter celery rotation. The six treatments in the study included: one complete chemical fertilizer (4/4CN) treatment and five organic substitution treatments (3/4CN+1/4MN, 2/4CN+2/4MN, 1/4CN+3/4MN, 2/4CN+1/4MN+1/4SN, 2/4CN+2/4SN), MN and SN represented the nitrogen from pig manure and maize straws. All treatments had same amounts of N, P₂O₅, and K₂O. At the 20^th vegetable season, surface soil samples (0–20 cm) were collected for the determination of microbial community composition.

Results Compared with 4/4CN treatment, organic substitution treatments significantly increased soil microbial biomass C (MBC), N (MBN) and abundances of bacteria and fungi, but decreased the abundance of archaea. The abundances of bacteria and fungi in high C-amended treatments (1/4CN+3/4MN, 2/4CN+1/4MN+1/4SN, and 2/4CN+2/4SN) were higher than those in low C-amended treatments (3/4CN+1/4MN and 2/4CN+2/4MN), whereas the abundance of archaea was on the opposite. Organic-amendments increased the Shannon indices of archaea by 9.0%, while those of bacteria and fungi did not significantly change in 3/4CN+1/4MN and 2/4CN+2/4MN. At the phylum level of bacteria, organic-amended treatments had higher relative abundance of Proteobacteria, and lower relative abundance of Actinobacteria and Chloroflexi than 4/4CN treatment. Among the main dominant fungal taxa, organic-amended treatments induced higher relative abundance of Ascomycota, Chytridiomycota and Glomeromycota, and lower relative abundance of Basidiomycota. Among the main dominant archaea taxa, organic-amended treatments resulted in higher relative abundance of Euryarchaeota and Candidatus Bathyarchaeota, and lower relative abundance of Thaum archaeota. Principal component analysis showed that the archaea community composition was more sensitive to fertilization than bacterial and fungal community composition. Redundancy analysis (RDA) revealed that organic carbon explained 22.3%, 10.4%, and 36.0% of the variation in community structure of bacteria, fungi and archaea, respectively. RDA also showed that nitrate nitrogen explained 16.1%, 8.9% and 34.7% of the variation in community structures of bacteria, fungi, and archaea, respectively.

Conclusions Under the equal NPK input conditions, partial substitution of chemical fertilizer with organic amendments increases the abundances of bacteria and fungi, decreases archaea abundance, influences soil dominant flora composition and increases soil microbial diversity. Nitrate nitrogen and organic carbon are the two main soil factors that influence the variation of soil bacteria, fungi and archaea community structures. The archaea community composition is more sensitive to fertilization than bacterial and fungal ones. Overall, the fertilization mode of 2/4CN+1/4MN+1/4SN leads to most diverse and abundant microbial community structure which is good for maintaining soil health and high-yield of vegetables.