Strong shift in the diazotrophic endophytic bacterial community inhabiting rice (Oryza sativa) plants after flooding

Abstract

Flooding impacts soil microbial communities, but its effect on endophytic communities has rarely been explored. This work addresses the effect of flooding on the abundance and diversity of endophytic diazotrophic communities on rice plants established in a greenhouse experiment. The nifH gene was significantly more abundant in roots after flooding, whereas the nifH gene copy numbers in leaves were unaffected and remained low. The PCA (principal component analysis) of T-RFLP (terminal restriction fragment length polymorphism) profiles indicated that root communities of replicate plots were more similar and diverse after flooding than before flooding. The nifH libraries obtained by cloning and 454 pyrosequencing consistently showed a remarkable shift in the diazotrophic community composition after flooding. Gammaproteobacteria (66-98%), mainly of the genus Stenotrophomonas, prevailed in roots before flooding, whereas Betaproteobacteria was the dominant class (26-34%) after flooding. A wide variety of aerotolerant and anaerobic diazotrophic bacteria (e.g. Dechloromonas, Rhodopseudomonas, Desulfovibrio, Geobacter, Chlorobium, Spirochaeta, Selenomonas and Dehalobacter) with diverse metabolic traits were retrieved from flooded rice roots. These findings suggest that endophytic communities could be significantly impacted by changes in plant-soil conditions derived from flooding during rice cropping.

The role of water in plant–microbe interactions

“…Water flooding also affects rhizosphere microbes. In a controlled greenhouse experiment, a significant decrease in the overall microbial population was observed after flooding (Unger et al ., ; Ferrando and Fernandez Scavino, ). Flooding might also change the movement and distribution of microbes in soils and damage plant tissues, potentially creating wounds through which microbes can enter plants.…”

“…Water flooding also affects rhizosphere microbes. In a controlled greenhouse experiment, a significant decrease in the overall microbial population was observed after flooding (Unger et al, 2009;Ferrando and Fernandez Scavino, 2015). Flooding might also change the movement and distribution of microbes in soils and damage plant (a) A land plant takes up water from the soil by roots, distributes water through the xylem to other parts of the plant, and transpires water vapor into the atmosphere from the leaves.…”

Investigación de microorganismos promotores del crecimiento vegetal en cultivos de interés agronómico mediante análisis metagenómico y microbiológico

“…La descripción de los microorganismos presentes en el ambiente experimentó un gran avance gracias a la información que proporcionan los análisis basados en secuencias ribosomales o funcionales, y ha permitido establecer firmas moleculares a varios niveles taxonómicos, las que son utilizadas como la base de una identificación bacteriana por comparación filogenética [118]. Esta aproximación se ha utilizado para caracterizar la diversidad bacteriana en diferentes tipos de ambientes [119]- [122].…”

Effects of strategic tillage and plant hormone treatments on wheat-associated microbial communities

“…Gammaproteobacteria of the genera Enterobacter and Pseudomonas are the dominant endophytic bacteria on different plants, including tuberous roots of sweet potato (Marques et al, 2015), rice roots (Ferrando & Scavino, 2015;Ren et al, 2015a;Sessitsch et al, 2012), and the roots of mature trees of Populus deltoids (Gottel et al, 2011). The predominance of one or two operational taxonomic units (OTUs) in specific plant tissues has been reported after endophytic bacterial sequencing, such as a pseudomonas-like OTU in the roots of P. deltoids (Gottel et al, 2011) and two OTUs affiliated to Pseudomonas and Enterobacter in sugarcane stems (Magnani et al 2013).…”

“…Moreover, endophytic communities inhabiting leaves at different locations in the plant (upper or lower leaf) respond differentially to elevated CO 2 . Oxygen availability also exerts effects on endophytic bacterial communities in rice, especially on diazotrophs (Ferrando & Scavino, 2015).…”