Sulfur Fertilization Changes the Community Structure of Rice Root-, and Soil- Associated Bacteria

Abstract

Under paddy field conditions, biological sulfur oxidation occurs in the oxidized surface soil layer and rhizosphere, in which oxygen leaks from the aerenchyma system of rice plants. In the present study, we examined community shifts in sulfur-oxidizing bacteria associated with the oxidized surface soil layer and rice roots under different sulfur fertilization conditions based on the 16S ribosomal RNA (rRNA) gene in order to explore the existence of oligotrophic sulfur-oxidizing bacteria in the paddy rice ecosystem. Rice plants were grown in pots with no fertilization (control) or CaCO3 or CaSO4 fertilization. A principal-coordinates analysis (PCoA) showed that CaSO4 fertilization markedly affected bacterial communities associated with rice roots and soil, whereas no significant differences were observed in plant growth among the fertilizer treatments examined. In rice roots, the relative abundance of Acidobacteria, Alphaproteobacteria, Gammaproteobacteria, and TM7 was significantly higher in CaSO4-fertilized pots than in control pots. Alphaproteobacteria, Bradyrhizobiaceae, and Methylocystaceae members were significantly more abundant in CaSO4-fertilized roots than in control roots. On the other hand, the abundance of Actinobacteria and Proteobacteria was lower in CaSO4-fertilized soil than in control soil. These results indicate that the bacteria associated with rice roots and soil responded to the sulfur amendment, suggesting that more diverse bacteria are involved in sulfur oxidation in the rice paddy ecosystem than previously considered.

Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea

“…This discrepancy could be due to primer bias; the primers used for soxB gene amplification amplify the soxB genes of Epsilonproteobacteria and Chloroflexi very poorly ( Meyer and Kuever, 2007 ). In addition, Bradyrhizobiaceae within Alphaproteobacteria and Burkholderiaceae within Betaproteobacteria were the dominant families in our study area; however, previous research revealed that these families might adapt to oligotrophic sulfur environments, such as soil ( Jung et al, 2005 ; Masuda et al, 2010 ) and rhizosphere soils ( Anandham et al, 2008 ; Masuda et al, 2016 ). Therefore, further study is required to determine whether the families described here are the result of contamination or actually exist.…”

Growing Interest in Microbiome Research Unraveling Disease Suppressive Soils against Plant Pathogens

“…Microbiome studies were popularized by their focus on human health, particularly the intestinal microbiota (9). They have since been applied not only to soils, but also to plant shoot and root microbiomes (31) and have provided important insights into microbial community functions in the biogeochemical cycles of carbon (10), nitrogen (25), and sulfur (15). A metatranscriptomic analysis may reveal functional microbial populations and genetic components in soil microbiomes.…”

Plant-Associated Microbes: From Rhizobia To Plant Microbiomes

“…Amplicon sequence analyses of the 16S rRNA gene indicated that rice root microbiomes responded to Azospirillum sp. B501 inoculations ( 2 ) and sulfur amendments ( 23 ). The abundance of uncharacterized phylum ™7 members in rice roots was increased by sulfur amendments ( 23 ).…”

“…B501 inoculations ( 2 ) and sulfur amendments ( 23 ). The abundance of uncharacterized phylum ™7 members in rice roots was increased by sulfur amendments ( 23 ). In addition, an inoculation experiment of non-photosynthetic Bradyrhizobium sp.…”