In Situ Stable Isotope Probing of Methanogenic Archaea in the Rice Rhizosphere

Abstract

Microorganisms living in anoxic rice soils contribute 10 to 25% of global methane emissions. The most important carbon source for CH4 production is plant-derived carbon that enters soil as root exudates and debris. Pulse labeling of rice plants with 13CO2 resulted in incorporation of 13C into the ribosomal RNA of Rice Cluster I Archaea in the soil, indicating that this archaeal group plays a key role in CH4 production from plant-derived carbon. This group of microorganisms has not yet been isolated but appears to be of global environmental importance.

Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil

“…In this study, Methanobacteriaceae were favored in the treatments with straw application, which could be explained by variation of H 2 concentration (Lu and Conrad 2005;Peng et al 2008), indicating that Methanobacteriaceae contributed to CH 4 production in straw-applied rice field soil.…”

“…This shift could be explained by the change of H 2 concentration in the headspace. Low H 2 concentrations were favored Methanocellaceae (Lu and Conrad 2005;Peng et al 2008). Previous studies found that Methanocellaceae predominated methanogenic activity at high temperatures (e.g., 45°C) (Peng et al 2008;Lu et al 2015).…”

“…Methanocellaceae are known as RC-I methanogens and play a key role in CH 4 production in paddy soil (Lu and Conrad 2005). Hydrogenotrophic Methanocellaceae were favored in nitrate treatments in early incubation stage (on day 5) in both gene and transcript levels.…”

Molecular eco-systems biology: towards an understanding of community function

“…Functional assays of samples (for example, using BIOLOG plates to measure ecosystem substrateusage phenotypes) can provide insights into some of the processes that occur in communities, but do not provide information on which community members are involved. Techniques such as RNA-based stable-isotope probing [11,12], fluorescence in situ hybridization (FISH)-microautoradiography [13], isotope arrays [14] and FISHsecondary-ion mass spectrometry [15] and its variants [16] allow substrate usage and specific processes to be linked to species, but are limited to particular substrates, are subject to cross-feeding, are not applicable in all environments and do not generally provide molecular details on the genes that are involved [17]. Environmental DNA cloning and screening enable specific ecosystem functions to be linked to genes [18], but such linking to bacterial or archaeal species is rare, and when successful, necessitates the co-cloning of a phylogenetic marker [19].…”

“…Functional assays of samples (for example, using BIOLOG plates to measure ecosystem substrateusage phenotypes) can provide insights into some of the processes that occur in communities, but do not provide information on which community members are involved. Techniques such as RNA-based stable-isotope probing [11,12] Environmental shotgun sequencing [23][24][25][26][27] has recently provided ecosystems biology with a possible global 'onedoes-all' method. The random sampling of sequence data from the combined community members (the metagenome) provided a first unbiased and large-scale glimpse into the total molecular parts list of communities, and allowed the researchers (in theory) to simultaneously investigate genes, their functions and the individuals that exert them [23].…”