Comparative Metatranscriptomics of Rhizosphere Microbiomes in Survived and Dead Cocoa Plants Under Drought Condition

Abstract

Plant rhizosphere is an important ecological niche in which complex plant–microbe interactions occur. The rhizosphere microbial community has high genetic diversity, acting as an important regulator of plant productivity and growth, especially under stress conditions. This study reports the investigation of the rhizosphere community and their interactions under drought conditions in Theobroma cacao (cocoa), an important cash crop and commodity worldwide. We compared the active microbial community of the dead and survived cocoa plants under drought conditions using a metatranscriptomic approach. The metatranscriptome of four rhizosphere samples (two from drought plants and two from dead plants) was analysed. Based on mRNA annotation, the dominant taxa in the rhizosphere revealed Proteobacteria as the major phyla in all rhizosphere samples. The order of the top abundant phyla in rhizosphere of the surviving cocoa plant was Proteobacteria (42–49%), Firmicutes (0.4–2%), Actinobacteria (0.8–1.3%) and Acidobacteria (0.3–0.4%) whereas the rhizosphere of the dead plant revealed Proteobacteria (38–46%), Firmicutes (0.1–1.5%), Acidobacteria (0.7–0.9%) and Thaumarchaeota (0.3–0.5%). The microbial profiles of both rhizosphere samples were similar at the phylum level. Further analysis at the genus level revealed 1712 classified genera in the rhizosphere samples, at which all rhizosphere samples shared 739 genera. The most dominant genus identified was Pseudomonas, followed by Bacillus and Thiocapsa in rhizospheres of the surviving cocoa plants and Pseudomonas, followed by Aeromonas and Klebsiella in rhizospheres of the dead cocoa plants, respectively. Our results suggested changes in the microbial composition and structure in the rhizosphere of the cocoa plant, which might play important roles in the plant’s survival due to drought.