Deciphering the relative importance of soil and plant traits on the development of rhizosphere microbial communities

Rhizosphere microbes are critical for plant growth and vitality, but the structure of the root-associated microbial community varies due to site-specific soil factors and plant traits. Here, we investigated how soil type and plant species affect the rhizosphere microbial community. Soil types were collected from a rice field or a secondary forest. Each soil was planted with either pathogen-inoculated or un-inoculated seeds of Fusarium wilt-susceptible (watermelon and cucumber) or Fusarium wilt-resistant (celery) crops. Analysis of the rhizosphere microbial communities revealed differences in the same crop that was planted on different soil types, as well as between crops grown on the same soil type. Thus, there are soil-specific and plant species-specific factors that determine the rhizosphere microbial community structure. However, we found that the plant species effect on microbial community structure (explaining 18.1% of the variance in bacterial species and 13.3% of variance in fungal species) was less than the soil type effect (variance explained: 47.1% for bacteria, 29.2% for fungi). Notably, soil NH4+-N concentration was the most influential soil-specific factor affecting rhizosphere microbial community composition. The rhizosphere of each plant species harbored core and unique microbes that were different in their relative abundance and composition. The pathogen-inoculated plants had a similar rhizosphere microbial community as those that were not inoculated with Fusarium wilt-causing fungus, although there was an increase in the relative abundances of microbial genera associated with biological disease control and maintenance of plant health. We conclude that the rhizosphere microbial community structure is determined more by soil type than the plant species cultivated in that soil.