Microbiome structure variation and soybean's defense responses during flooding stress and elevated CO₂

With current trends in global climate change, both flooding episodes and higher levels of CO₂ have been key factors to impact plant growth and stress tolerance. Very little is known about how both factors can influence the microbiome diversity and function, especially in tolerant soybean cultivars. This work aims to (i) elucidate the impact of flooding stress and increased levels of CO₂ on the plant defenses and (ii) understand the microbiome diversity during flooding stress and elevated CO₂ (eCO₂).

We used next-generation sequencing and bioinformatic methods to show the impact of natural flooding and eCO₂ on the microbiome architecture of soybean plants' below- (soil) and above-ground organs (root and shoot). We used high throughput rhizospheric extra-cellular enzymes and molecular analysis of plant defense-related genes to understand microbial diversity in plant responses during eCO₂ and flooding.

Results revealed that bacterial and fungal diversity was substantially higher in combined flooding and eCO₂ treatments than in non-flooding control. Microbial diversity was soil>root>shoot in response to flooding and eCO₂. We found that sole treatment of eCO₂ and flooding had significant abundances of Chitinophaga, Clostridium, and Bacillus. Whereas the combination of flooding and eCO2 conditions showed a significant abundance of Trichoderma and Gibberella. Rhizospheric extra-cellular enzyme activities were significantly higher in eCO₂ than flooding or its combination with eCO₂. Plant defense responses were significantly regulated by the oxidative stress enzyme activities and gene expression of Elongation factor 1 and Alcohol dehydrogenase 2 in floodings and eCO₂ treatments in soybean plant root or shoot parts.

This work suggests that climatic-induced changes in eCO₂ and submergence can reshape microbiome structure and host defenses, essential in plant breeding and developing stress-tolerant crops. This work can help in identifying core-microbiome species that are unique to flooding stress environments and increasing eCO₂.