Different Bacterial Populations Associated with the Roots and Rhizosphere of Rice Incorporate Plant-Derived Carbon

Abstract

Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH 4 , which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with 13 CO 2 for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with 13 C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria classes of Proteobacteria and the "Spartobacteria" and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (ϳ20%) than did those in the rhizosphere (ϳ4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment. The interaction between plants and microorganisms within the root and in the rhizosphere is complex and poorly understood. Early studies focused on specific plant growth-promoting bacteria (1, 2) and more recently on characterizing the rhizosphere microbial community (3). For example, studies with Arabidopsis thaliana, a model plant species, have shown that the root endophytic microbial communities are highly specific (4, 5). In rice, the microbial communities associated with the rhizosphere and the phyllosphere have been characterized by a metaproteogenomic approach (6), and a metagenomic approach was used to characterize the endophytic root community in rice (7).A variety of factors act to shape the microbial community within the roots and in the rhizosphere, including the volume and nature of carbon substrates transported by the plant to the roots (8) and highly evolved signaling and interaction mechanisms between plants and microbes and the plant immune system (9). Plants actively recruit and sustain microorganisms in the root environment in part by the translocation of organic compounds from the leaves to the roots and into the rhizosphere that serve as growth substrates. In annual plants, this has been shown to account for 30 to 60% of net fixed carbon, 40 to 90% of which is excreted by the root and ultimately sequestered or respired by the root-associated microorganisms (10)....

Isolation and Studies on Bacterial Endophytes from Two Venezuelan Rice Cultivars

“…Profiling the bacterial communities allowed us to determine that the rhizospheres of both rice cultivars were more diverse than the endorhizospheres, an observation widely documented [37], [38]. Proteobacteria were by far the most predominant group in both compartments of both rice varieties, and this is in agreement with several previous studies [14][15] [39].…”

“…Interesting Opitutus sp. is obligate anaerobic with fermentative metabolism that utilizes rice plant-derived carbons [37]. The presence of anaerobic microbes within the plant, an environment which is O2-rich, seems paradoxical and was also reported by [39].…”

Giving back to the community: microbial mechanisms of plant–soil interactions

“…Furthermore, stable isotope probing data indicate that carbon fixed by the plant via photosynthesis is directly incorporated by specific bacterial taxa in the rhizosphere (Hernández et al . ) and that this assimilation is dependent in close proximity to the root (Lu, Abraham & Conrad ).…”

The effect of crop rotation between wetland rice and upland maize on the microbial communities associated with roots

“…Furthermore, composition depends on how the root microbial community is assessed, which basically is the extraction protocol. Thus, the root microbial community can be differentiated from inside to outside as endophytic (inside the root tissue), ectophytic (on the rhizoplane, i.e., the ectorhizosphere), and rhizospheric (soil particles firmly attached to the root surface) (Edwards et al 2015;Hernandez et al 2015).…”