Effects of Elevated Carbon Dioxide, Elevated Temperature, and Rice Growth Stage on the Community Structure of Rice Root–Associated Bacteria

Abstract

The effects of free-air carbon dioxide enrichment (FACE) and elevated soil and water temperature (warming) on the rice root–associated bacterial community were evaluated by clone library analysis of the 16S ribosomal RNA gene. Roots were sampled at the panicle initiation and ripening stages 41 and 92 days after transplanting (DAT), respectively. The relative abundances of the methanotrophs Methylosinus and Methylocystis were increased by warming and decreased by FACE at 92 DAT, which indicated that microbial methane (CH4) oxidation in rice roots may have been influenced by global warming. The relative abundance of Burkholderia kururiensis was increased by warming at 41 DAT and by FACE or warming at 92 DAT. The abundances of methanotrophs increased during rice growth, which was likely induced by an enhancement in the emission of CH4 from the paddy fields, suggesting that CH4 is one of the predominant factors affecting the structure of the microbial community in rice roots. Marked variations in the community structure were also observed during rice growth in other genera: Bradyrhizobium, Clostridium, and an unknown genus close to Epsilonproteobacteria were abundant at 92 DAT, whereas Achromobacter was abundant at 41 DAT. These results demonstrated that the community structures of rice root-associated bacteria were markedly affected by FACE, temperature, and the rice growth stage.

Symbiosis Island Shuffling with Abundant Insertion Sequences in the Genomes of Extra-Slow-Growing Strains of Soybean Bradyrhizobia

“…Bradyrhizobia prefer legumes (34,35) and nonlegumes (36)(37)(38) that tend to form symbiosis (39). The present study advances genomic characterization of HRS strains of soybean bradyrhizobia with abundant ISs.…”

Short-term response of nitrifier communities and potential nitrification activity to elevated CO2 and temperature interaction in a Chinese paddy field

“…Root biomass and tiller number of wild rice were reported to significantly increase under elevated CO 2 (Inubushi et al, 2003;Kim et al, 2003). Accordingly, increased carbon input in the rhizosphere soil though rice root exudates and rhizodeposition was observed under elevated CO 2 (Bhattacharyya et al, 2013;Okubo et al, 2014). As microbial communities in soil can be generally mediated by carbon substrate availability, an increase in below-ground carbon input could bring changes in soil microbial biomass under climate change conditions (Rakshit et al, 2012).…”

“…Effects had been frequently reported of CO 2 enrichment on rice ecosystem function including rice grain yield and quality, plant nutrients uptake and greenhouse gas emission (Hasegawa et al, 2013;Usui et al, 2014;Tokida et al, 2011). Correspondingly, activity and community composition of ammonia oxidizer in rice rhizosphere could be affected by elevated CO 2 through root exudates and rhizodeposition as well as soil organic carbon (Bhattacharyya et al, 2013;Okubo et al, 2014). The changes to nitrifying activity of agricultural soils under elevated atmospheric CO 2 and warming conditions had been shown to depend on soil pH, inorganic N availability, and ammonia oxidizer community structure and abundance, but these changes were difficult to correlate with those in nitrifying activity (Yao et al, 2011;Long et al, 2012).…”

Phylogeny and Functions of Bacterial Communities Associated with Field-Grown Rice Shoots

“…Numerous ecological studies utilizing culture-dependent and -independent analyses have been conducted to investigate these rice-associated microbes (3, 14). These studies revealed the diversity as well as functions of rice-associated microbes.…”