Methanogen community in flooded paddy soil

Co-occurrence network analyses for 30°C (a) and 45°C (b). Nodes were colored by modularity class with labeled family names. Each connection (edge) between two nodes stands for a strong (Spearman’s 0.6≤ρ≤0.9) and significant (FDR corrected P value < 0.01) correlation. The size of each node is proportional to the number of connections (its degree). Designation of the major modules (LM: low-temperature module; HM: high-temperature module) is shown in red bold color. (c) Temporal dynamics of dominant families (> 1% relative abundance) in different modules at 30°C (LM4-6 [low-complexity modules], LM2, LM3) and 45°C (HM1, HM2, HM3). The figure was taken from Peng et al. (2018).

The expected increase in global surface temperature (2-4°C by 2050) due to climate change may have a tremendous impact on the structure and function of the anaerobic food web in flooded rice field soil. Although the in situ temperature in paddy soils is generally lower than or around 30°C, present-day temperatures above 40°C are reached in rice fields of Southeast Asia. We applied environmental transcriptomics, or metatranscriptomics, to investigate the effects of rising temperature (30°C vs 45°C) on the methanogenic food web in flooded, rice straw-amended paddy soil (Peng et al., 2018). In another project, we assessed how drainage affects microbiota structure and function in rice field soil. Drainage is an important mitigation strategy to reduce methane emission from rice paddies (Abdallah et al., 2019).


Mesophilic (30 °C) and thermophilic (45 °C) food web communities had a modular structure (Figure). Temperature had a differential effect on all the functional activities, including polymer hydrolysis, syntrophic oxidation of key intermediates, and methanogenesis. At 30°C, various bacterial phyla contributed to polymer hydrolysis, with Firmicutes decreasing and non-Firmicutes (e.g., Bacteroidetes, Ignavibacteriae) increasing with incubation time. At 45°C, CAZyme expression was solely dominated by Firmicutes but, depending on polymer and incubation time, varied on family level. At both temperatures, a major change in food web functionality was linked to the transition from an early stage to a later stage of rice straw degradation. The mesophilic food web was characterized by gradual polymer breakdown that governed acetoclastic methanogenesis (Methanosarcinaceae) and, with polymer hydrolysis becoming the rate-limiting step, syntrophic propionate oxidation (Christensenellaceae, Peptococcaceae). The thermophilic food web had two activity stages characterized first by polymer hydrolysis and followed by syntrophic oxidation of acetate (Thermoanaerobacteraceae, Heliobacteriaceae, clade OPB54). Hydrogenotrophic Methanocellaceae was the syntrophic methanogen partner, but its population structure differed between 30°C and 45°C. In conclusion, temperature had a differential effect on the structural and functional continuum in which the methanogenic food web operates. This temperature-induced change in food web functionality may not only be a near-future scenario for rice paddies but also for natural wetlands in the tropics and subtropics.


Soil microcosms were pre-incubated for 28 days under flooded conditions followed by nine-day drainage. With drainage, oxygen concentration increased from suboxic (1.6 µmol/l) to near-atmospheric (240 µmol/l) levels. Concurrently, water potential decreased to -0.87 MPa (corresponding to 11% soil moisture content). Drainage did not affect the absolute (RT-qPCR) SSU rRNA abundances of Bacteria and Archaea, but changed significantly their community composition. Firmicutes (Clostridiaceae, Ruminococcaceae, Lachnospiraceae) decreased, while Actinobacteria (Nocardioidaceae) and Proteobacteria (Comamonadaceae) increased in relative abundance. These taxon-specific changes were observed on both rRNA and mRNA levels. Methanogen SSU rRNA abundance was stable, but methanogen mRNA significantly decreased in abundance. This coincided with complete depression of the methane production potential in drained soil. Among Eukarya, protists and Amoebozoa thrived in flooded soil, while Fungi proliferated with drainage. Taking community-wide mRNA expression as a proxy, the overall microbial activity was not severely affected by drainage. In particular, the abundance of mRNA involved in transcription and translation significantly increased. Correspondingly, the bacterial SSU rRNA transcript/gene ratio increased 12-fold with drainage, suggesting the development of a metabolically active microbial community well adapted to oxic and dry soil conditions. This community showed an increased transcription of genes involved in degrading lignin, peptidoglycan, and storage molecules such as glycogen.  



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