Long-Term Greenhouse Cucumber Production Alters Soil Bacterial Community Structure

Long-term intensive greenhouse production commonly leads to continuous cropping obstacles and therefore declines the productivity of greenhouse system, soil microbiological mechanisms behind which remain poorly understood so far. Here, based on a continuous greenhouse cucumber cropping system, the differences in bacterial community structure of the soils with different cucumber cultivation history were assessed through high-throughput sequencing. The beta diversity of bacterial community, but not alpha diversity, significantly changed as consecutive cucumber cultivation and also positively linked to cucumber yield. As for bacterial community members, at phylum level, prolonged cucumber cultivation increased average relative abundances of Chloroflexi and Gemmatimonadetes while decreasing average relative abundance of Nitrospirae; at genus level, continuous cucumber cultivation decreased average relative abundances of some beneficial microbes (i.e. Bacillus, Solirubrobacter, and Rubrobacter) and N-cycling related microbes (i.e. Nitrospira and Azoarcus) while increasing average relative abundance of some functional microbes (i.e. Agromyces, Thermomicrobium, Desulfotomaculum, Sphaerobacter, and Mycobacterium). Soil available phosphorus and organic carbon contents were the most important contributors to the shifts of bacterial community structure. Co-occurrence network analysis indicated long-term greenhouse cucumber cultivation weakened the interaction of species within bacterial community and led to less complex and connected organization among bacterial taxa. Overall, our results suggested that soil bacterial community structure and the interactions of bacterial taxa may play the important roles in the occurrence of continuous cropping obstacles in a long-term intensive greenhouse production system.