Methane Production in Soil Environments—Anaerobic Biogeochemistry and Microbial Life between Flooding and Desiccation

Abstract

Flooding and desiccation of soil environments mainly affect the availability of water and oxygen. While water is necessary for all life, oxygen is required for aerobic microorganisms. In the absence of O2, anaerobic processes such as CH4 production prevail. There is a substantial theoretical knowledge of the biogeochemistry and microbiology of processes in the absence of O2. Noteworthy are processes involved in the sequential degradation of organic matter coupled with the sequential reduction of electron acceptors, and, finally, the formation of CH4. These processes follow basic thermodynamic and kinetic principles, but also require the presence of microorganisms as catalysts. Meanwhile, there is a lot of empirical data that combines the observation of process function with the structure of microbial communities. While most of these observations confirmed existing theoretical knowledge, some resulted in new information. One important example was the observation that methanogens, which have been believed to be strictly anaerobic, can tolerate O2 to quite some extent and thus survive desiccation of flooded soil environments amazingly well. Another example is the strong indication of the importance of redox-active soil organic carbon compounds, which may affect the rates and pathways of CH4 production. It is noteworthy that drainage and aeration turns flooded soils, not generally, into sinks for atmospheric CH4, probably due to the peculiarities of the resident methanotrophic bacteria.

More Than a Methanotroph: A Broader Substrate Spectrum for Methylacidiphilum fumariolicum SolV

“…About 70–80% of CH 4 is generated biologically and a large part of it is removed in the stratosphere and troposphere through reactions with chlorine and ⋅ OH radicals ( Le Mer and Roger, 2001 ). In addition, microbial methane oxidation is an important terrestrial methane sink ( Conrad, 2020 ). Bacteria can convert CH 4 to methanol aerobically using the enzyme methane monooxygenase (MMO; Conrad, 2009 ).…”

Effect of water management on microbial diversity and composition in an Italian rice field system

“…Our study site in Vercelli (Italy) has a history of rice cultivation for over a century (Ferrero and Vidotto 2010 ) and thus, these soils have been exposed to many cycles of flooding and drainage. Over time, a soil community has been selected that is adapted to these conditions (Conrad 2020 ). It has been shown that microbial communities in rice fields stayed rather stable after drainage or re-flooding and even methanogenic archaea did not decrease considerably in numbers after desiccation and oxygen exposure (Breidenbach et al 2016 , Liu et al 2018 , Conrad 2020 ).…”

“…Over time, a soil community has been selected that is adapted to these conditions (Conrad 2020 ). It has been shown that microbial communities in rice fields stayed rather stable after drainage or re-flooding and even methanogenic archaea did not decrease considerably in numbers after desiccation and oxygen exposure (Breidenbach et al 2016 , Liu et al 2018 , Conrad 2020 ). This agrees with our study and the observation that the overall microbial composition in the bulk soil was only weakly affected by the different water management.…”

Transcriptional dynamics of methane-cycling microbiomes are linked to seasonal CH4 fluxes in two hydromorphic and organic-rich grassland soils

“…The water content of soils directly affects O2 availability, which, in turn, is a fundamental factor shaping CH4-cycling community composition. O2 diffuses more slowly in water-saturated soils, which thus have lower O2 availability [56].…”