The impact of differential temperatures (30°C versus 45°C) on the methanogenic community in Philippine rice field soil

Methanogenese ist eine der bedeutendsten biogenen Quellen für atmosphärisches Methan (CH4). Dieses ist nach Kohlendioxid das zweitwichtigste Treibhausgas. Insbesondere geflutete Reisfelder sind mit einem Beitrag von circa 25% zur jährlichen Methanemission in die Erdatmosphäre eine kritische anthropo...

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Bibliographic Details
Main Author: Li, Xin
Contributors: Liesack, Werner (Prof. Dr.) (Thesis advisor)
Format: Doctoral Thesis
Language:English
Published: Philipps-Universität Marburg 2023
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Microbial methanogenesis is the largest biogenic source of atmospheric methane (CH4), which is the second most important anthropogenic greenhouse gas. In particular, water-logged rice paddies contribute approximately 25% to the total annual CH4 budget in the atmosphere, making them a critical source of anthropogenic CH4 emissions into earth’s atmosphere. The methanogenic degradation of organic matter in anoxic environments, whose final products are methane and carbon dioxide, contributes to the energy flow and circulation of matter in ecosystems and involves a microbial food chain composed of different functional guilds of the domains Bacteria and Archaea. But a deep understanding of their activity dynamics during the methanogenic organic matter breakdown in Philippine paddy soil has not yet been achieved. In addition, like most other forms of metabolism, methanogenesis is temperature-dependent. The expected increase in global surface temperature due to climate change may have a tremendous effect on the microbial dynamics and methanogenic processes in flooded rice field soil. However, a system-level understanding of the effects of rising temperature on the anaerobic food chain in Philippine paddy soil is still lacking. Anoxic paddy soil slurries amended with rice straw were used as model system. A multi-methods approach (the combination of metabolite measurements, quantitative analysis of biomarkers, metatranscriptomics analysis, and metagenomics analysis) was applied to decipher the compositional and functional dynamics of the methanogenic community in Philippine rice field soil over an incubation period of 120 days under mesophilic (30 ℃) and moderately thermophilic temperatures (45 ℃). In particular, we aimed at answering the following questions: (i) who are the major bacterial players at the different trophic levels of the anaerobic food chain; (ii) which methanogenic pathways dominate, and which methanogen groups are prevalent during the 120-day incubation period; and (iii) how does the rising temperature affect the structural and functional dynamics of the methanogenic community? At mesophilic temperature, qPCR and RT-qPCR, but also metatranscriptomics, revealed two major bacterial and methanogenic activity phases defined as early (days 7 to 21) and late (days 28 to < 60 days) community responses, separated by a significant transient decline in microbial gene and transcript abundances. Geobacteraceae was the most abundant bacterial population over incubation time. The two methanogenic activity phases corresponded to greatest transcript abundances of the Methanosarcinaceae, but differed in the methanogenic pathways expressed. While three genetically distinct Methanosarcina populations contributed ii to acetoclastic methanogenesis during the early activity phase, the late activity phase was defined by methylotrophic and acetoclastic methanogenesis performed by only a single Methanosarcina population. Mapping of environmental transcripts onto metagenome-assembled genomes (MAGs) revealed a population closely related to Methanosarcina sp. MSH10X1 to be the key player in both acetoclastic and methylotrophic methanogenesis. Members of the Methanocellaceae were the key players in hydrogenotrophic methanogenesis, while the acetoclastic activity of Methanotrichaceae members was detectable only during the very late community response. At moderately thermophilic temperature, the structure and function (including polymer hydrolysis, syntrophic oxidation of key intermediates, and methanogenesis) of the methanogenic community displayed differential responses compared to mesophilic temperature. Heliobacteriaceae replaced Geobacteraceae to prevail in bacterial dynamics during the 120-day incubation period. The transcript dynamics of CAZyme-encoding genes showed a different pattern, compared with mesophilic condition. In particular, CAZyme genes involved in the hydrolysis of cellulose and hemicellulose had an increased transcript activity in the late stage. The methanogen community and their dynamics were characterized by acetoclastic-methylotrophic (Methanosarcinaceae) and hydrogenotrophic (Methanocellaceae) methanogens. The intra-family analysis of Methanosarcinaceae identified five genetically distinct Methanosarcina populations that differed in the methanogenic pathways expressed. Mapping of environmental transcripts onto Methanosarcina reference genomes revealed that two Methanosarcina populations mainly contributed to acetoclastic and methylotrophic methanogenesis during the early activity phase. These were closely affiliated to Methanosarcina flavescens - Methanosarcina thermophila TM-1 and Methanosarcina barkeri 3, respectively. The late activity phase was defined only by methylotrophic methanogenesis, which was performed by a single Methanosarcina population closely affiliated to Methanosarcina barkeri 3. Members of the Methanocellaceae were the key players in hydrogenotrophic methanogenesis, while no acetoclastic activity of Methanotrichaceae members was observed under moderately thermophilic condition. In conclusion, the occurrence of methylotrophic methanogenesis, in addition to acetoclastic and hydrogenotrophic methanogenesis, at both mesophilic and moderately thermophilic temperatures is a crucial new finding. Temperature had a differential effect on the structural and functional continuum in which the methanogenic food chain operates. Our study showed that the methanogenic community responses in flooded rice field soils are more complex than previously thought.