Active community structure of microeukaryotes in a rice (Oryza sativaL.) rhizosphere revealed by RNA-based PCR-DGGE

Abstract

The rhizosphere is one of the hot spots in soil ecosystems for a variety of microorganisms. In this study, we explored the seasonal change of the microeukaryotic community of a rice rhizosphere focusing on the active members through an RNA-based molecular approach. Rice plants (Oryza sativa L.) were grown in a pot where the rhizosphere was compartmented from bulk soil with a nylon gauze. The Eh in the rhizosphere compartment indicated that the rhizosphere was under oxic conditions in the initial stage of plant growth and then suddenly became anoxic or suboxic. Denaturing gradient gel electrophoresis targeting 18S rRNA-transcribed cDNA demonstrated that the active community of microeukaryotes in the rice rhizosphere was different from that in the bulk soil. The rhizosphere community showed a temporal shift in accordance with the shift of the redox conditions having three stages: the oxic before maximum tillering stage, anoxic/suboxic stage before maximum tillering stage, and anoxic/ suboxic stage in the panicle initiation stage and thereafter. Active members specific to the rhizosphere at either the oxic or anoxic/suboxic stage were found: Heterolobosea amoeba, ciliates, and Chytridiomycota fungi for the oxic stage and oomycetes, ciliates and Ascomycota fungi in the anoxic/ suboxic stage. The present results demonstrate that a specific group of microeukaryotes inhabit the rice rhizosphere even under anoxic/suboxic conditions and play various ecological roles as plant parasites, microbial grazers and organic decomposers.

The effects of plant type, AMF inoculation and water regime on rhizosphere microbial communities

“…The effect of inoculation on the structure of microbial communities in wet soils could be related to increased exudates by the extraradical mycelium (their growth is inhibited under low soil moisture) or increased root exudation, further enhanced by the colonization of roots by AMF. The rhizosphere community of inoculated F. pratensis soils was dominated by bacteria and microeukaryotes, the latter being grazers of bacteria (Asiloglu & Murase, ). The paucity of fungal markers in inoculated F. pratensis rhizospheres supports the idea of competition between AM and free‐living fungi.…”

Quest of Soil Protists in a New Era

“…Publicly available metagenome data are less used for studying the diversity of soil microeukaryotes but can provide valuable information as they are free from the PCR biases and include the sequences of genes that are not targeted in amplicon-based approaches ( 34 ). The rhizosphere of plants is known to be a hot spot of soil protists ( 4 , 5 ) and the phyllosphere may be another important habitat for protists in terrestrial ecosystems ( 52 ).…”

Predatory Protists: The Key Players in the Quest for Sustainable Agricultural Practices

“…Plant pathogenic protists (mainly belonging to Oomycetes) cause enormous negative impacts on agricultural production, while negative effect on the health of animals and microorganisms caused by animal and microbial parasites belonging to protists (Gilbert & Parker 2023). Taken together, soil biodiversity, nutrient cycling, and agricultural productivity are controlled by protists and protist communities are sensitive to environmental factors such as soil physicochemical properties, the rhizosphere effect, organic and inorganic fertilizers, especially nitrogen (Asiloglu et al 2015;2016;2021a;2021b;Asiloglu 2022;Bodur et al 2024).…”