Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters

Abstract

Rice cultivation worldwide accounts for ∼7 to 17% of global methane emissions. Methane cycling in rice paddies is a microbial process not only involving methane producers (methanogens) and methane metabolizers (methanotrophs) but also other microbial taxa that affect upstream processes related to methane metabolism. Rice cultivars vary in their rates of methane emissions, but the influence of rice genotypes on methane cycling microbiota has been poorly characterized. Here, we profiled the rhizosphere, rhizoplane, and endosphere microbiomes of a high-methane-emitting cultivar (Sabine) and a low-methane-emitting cultivar (CLXL745) throughout the growing season to identify variations in the archaeal and bacterial communities relating to methane emissions. The rhizosphere of the high-emitting cultivar was enriched in methanogens compared to that in the low emitter, whereas the relative abundances of methanotrophs between the cultivars were not significantly different. Further analysis of cultivar-sensitive taxa identified families enriched in the high emitter that are associated with methanogenesis-related processes. The high emitter had greater relative abundances of sulfate-reducing and iron-reducing taxa which peak earlier in the season than methanogens and are necessary to lower soil oxidation reduction potential before methanogenesis can occur. The high emitter also had a greater abundance of fermentative taxa which produce methanogenesis precursors (acetate, CO2, and H2). Furthermore, the high emitter was enriched in taxa related to acetogenesis which compete with methanogens for CO2 and H2. These taxa were enriched in a spatio-specific manner and reveal a complex network of microbial interactions on which plant genotype-dependent factors can act to affect methanogenesis and methane emissions. IMPORTANCE Rice cultivation is a major source of anthropogenic emissions of methane, a greenhouse gas with a potentially severe impact on climate change. Emission variation between rice cultivars suggests the feasibility of breeding low-emission rice, but there is a limited understanding of how genotypes affect the microbiota involved in methane cycling. Here, we show that the root microbiome of the high-emitting cultivar is enriched both in methanogens and in taxa associated with fermentation, iron, and sulfate reduction and acetogenesis, processes that support methanogenesis. Understanding how cultivars affect microbes with methanogenesis-related functions is vital for understanding the genetic basis for methane emission in rice and can aid in the development of breeding programs that reduce the environmental impact of rice cultivation.

Drought duration determines the recovery dynamics of rice root microbiomes

“…The copyright holder for this preprint this version posted September 30, 2020. ; https://doi.org/10.1101/2020.09.29.314781 doi: bioRxiv preprint 12 allowing a succession of taxa that respire increasingly energetically unfavorable compounds [31].…”

Microbial Interactions Within Multiple-Strain Biological Control Agents Impact Soil-Borne Plant Disease

“…to build a rhizospheric microbial association, in which the Hyphomicrobium spp. is capable of removing methanol ( Liechty et al, 2020 ). Therefore, the promotion of the growth of rhizosphere microbes can be achieved by syntrophic interactions leading to effective nutrient utilization and removal of harmful substances ( Figure 1B ).…”

Bioactive diterpenoids impact the composition of the root-associated microbiome in maize (Zea mays)

“…After filtering to remove mitochondrial and chloroplast OTUs, 4,259 distinct OTUs remained. Following standard protocols for analyzing data with a binomial distribution, such as the MiSeq data generated in this study, OTU counts were normalized by relative abundance, in which the counts were taken as a percentage of the total number www.nature.com/scientificreports/ of OTU counts for a sample [33][34][35] . This method was used rather than rarefaction methods, which are at risk for discarding so as not to discard low abundance OTUs 36 .…”