Abstract
The subterranean microbiota of plants is of great importance for plant growth and health, as root-associated microbes can perform crucial ecological functions. As the microbial environment of roots is extremely diverse, identifying keystone microorganisms in plant roots, rhizosphere, and bulk soil is a necessary step towards understanding the network of influence within the microbial community associated with roots and enhancing its beneficial elements. To target these hot spots of microbial interaction, we used inter-kingdom network analysis on the canola growth phase of a long-term cropping system diversification experiment conducted at four locations in the Canadian Prairies. Our aims were to verify whether bacterial and fungal communities of canola roots, rhizosphere, and bulk soil are related and influenced by diversification of the crop rotation system; to determine whether there are common or specific core fungi and bacteria in the roots, rhizosphere, and bulk soil under canola grown in different environments and with different levels of cropping system diversification; and to identify hub taxa at the inter-kingdom level that could play an important ecological role in the microbiota of canola. Our results showed that fungi were influenced by crop diversification, which was not the case on bacteria. We found no core microbiota in canola roots but identified three core fungi in the rhizosphere, one core mycobiota in the bulk soil, and one core bacterium shared by the rhizosphere and bulk soil. We identified two bacterial and one fungal hub taxa in the inter-kingdom networks of the canola rhizosphere, and one bacterial and two fungal hub taxa in the bulk soil. Among these inter-kingdom hub taxa, Bradyrhizobium sp. and Mortierella sp. are particularly influential on the microbial community and the plant. To our knowledge, this is the first inter-kingdom network analysis utilized to identify hot spots of interaction in canola microbial communities.
Highlights
Plant subterranean microbiota have often been described as a “black box” [1,2,3,4]—a term referring to an inherent complexity of inner workings that makes a system difficult to grasp in its entirety
PERMANOVA conducted by site reported a significant effect of cropping system diversification on fungal communities in certain sites and microbiota compartments, but no significant effect of diversification on bacterial communities was detected in any compartment of the subterranean microbiota of canola (Table 2)
Our results support the existence of stable core bacterial and fungal components of the canola rhizosphere and in the bulk soil of canola-producing fields
Summary
Plant subterranean microbiota have often been described as a “black box” [1,2,3,4]—a term referring to an inherent complexity of inner workings that makes a system difficult to grasp in its entirety. We can define plant subterranean microbiota as composed of different biotopes, notably: the root interior, the rhizosphere, and the bulk soil. Rhizodeposits recruit root symbionts and shape the microbial community of the rhizosphere [5,6,7]. Microbial communities shaped by the plant in the rhizosphere and root interior can protect it against pathogens and enhance its growth and production [6, 8,9,10,11]. While important to plant health, are less influenced by the plant due to their distance from the roots. The microbes in the bulk soil can produce volatile compounds that influence plant health and development [13, 15,16,17]
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