Dynamics of the Methanogenic Archaeal Community during Plant Residue Decomposition in an Anoxic Rice Field Soil

Abstract

Incorporation of plant residues strongly enhances the methane production and emission from flooded rice fields. Temperature and residue type are important factors that regulate residue decomposition and CH 4 production. However, the response of the methanogenic archaeal community to these factors in rice field soil is not well understood. In the present experiment, the structure of the archaeal community was determined during the decomposition of rice root and straw residues in anoxic rice field soil incubated at three temperatures (15°C, 30°C, and 45°C). More CH 4 was produced in the straw treatment than root treatment. Increasing the temperature from 15°C to 45°C enhanced CH 4 production. Terminal restriction fragment length polymorphism analyses in combination with cloning and sequencing of 16S rRNA genes showed that Methanosarcinaceae developed early in the incubations, whereas Methanosaetaceae became more abundant in the later stages. Methanosarcinaceae and Methanosaetaceae seemed to be better adapted at 15°C and 30°C, respectively, while the thermophilic Methanobacteriales and rice cluster I methanogens were significantly enhanced at 45°C. Straw residues promoted the growth of Methanosarcinaceae, whereas the root residues favored Methanosaetaceae. In conclusion, our study revealed a highly dynamic structure of the methanogenic archaeal community during plant residue decomposition. The in situ concentration of acetate (and possibly of H 2 ) seems to be the key factor that regulates the shift of methanogenic community.Plant residues are a by-product of rice production. The incorporation of plant residues into rice field soil is a common practice in Asian agriculture that could help to maintain the soil fertility. However, the incorporation of plant residues strongly enhances the methane emissions from rice fields (8,13,38,39). It has been shown that the decomposition of straw residues in rice field soil is performed by a spatially wellorganized consortium: the hydrolysis and primary fermentation reactions are mainly localized on the straw residue while the syntrophic and methanogenic reactions occur in the adjacent soil (14). There was an astonishing richness of archaeal diversity present on rice roots and in the surrounding paddy soil (4,16,17,29). Although it was shown that the structure of methanogenic archaea in the rice field soil remained relatively constant over the growing season of rice plants (24), the incorporation of rice straw selectively enhanced the growth of Methanosarcinaceae and Methanobacteriales and suppressed rice cluster I (RC-I) methanogens and Methanomicrobiales (7). Apparently, the members of the methanogenic community respond differently to the incorporation of organic residues. Rice straw and root residues are the major forms of organic residues incorporated into rice field soils. It was shown that the decomposition of root residues was slower than straw residues (26). However, it is unknown whether such a difference in the rates of decomposition is also reflected in the structure ...

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

“…As reported in previous studies (Peng et al 2008;Lu et al 2015), our study showed that straw addition increased CH 4 production. The addition of nitrate with straw reduced CH 4 production compared with the treatment with straw alone.…”

“…A clear shift from Methanosarcinaceae to Methanosaetaceae was observed on day 5 in treatments with nitrate by analysis of transcripts. An expected change of acetate concentrations was observed in these treatments, with accumulation in the early stages of incubation with a subsequent decrease; this was strongly in accordance with earlier reports (Jetten et al 1992;Peng et al 2008). Moreover, higher levels of nitrate (NO 3 − ), nitrous oxide (N 2 O), and sulfate (SO 4 2− ) in the same p e r i o d i n t h e s e t r e a t m e n t s p r o b a b l y a f f e c t e d Methanosarcinaceae and Methanosaetaceae.…”

“…Based on analysis of mcrA genes, Methanosarcinaceae were found to be the predominant archaea of the methanogenic community, and straw addition (alone) stimulated their growth in the early stage of incubation, as observed previously (Peng et al 2008;Conrad et al 2012). Methanosarcinaceae are known as fast-growing and substrate-versatile methanogens and not only can use high concentrations (0.2-1.2 mM) of acetate, but also can utilize H 2 -CO 2 or methanol (Jetten et al 1990;Conrad 2007).…”

“…have been described as slow-growing methanogens, utilizing acetate over a lower range of concentrations (7-70 μM) (Jetten et al 1992). Methanosaetaceae are usually dominant when acetate concentrations decrease to a low level (Peng et al 2008). In this study, the relative abundance of Methanosaetaceae in gene level obviously increased in the Ctrl and nitrate-alone treatment on days 5 and 11.…”

“…However, incorporation of straw also increases CH 4 production and emissions (Denier Van Der Gon and Neue 1995;Zou et al 2005). Several incubation studies have shown a highly dynamic structure of methanogenic archaeal communities during straw decomposition, with members responding differently to organic residue type, incubation temperature, and duration of incubation (Conrad and Klose 2006;Peng et al 2008;Conrad et al 2012;Lu et al 2015). It is thought that the concentrations of acetate and H 2 are the key factors that control methanogenic community composition during the degradation of rice straw (Conrad 2007).…”