Methane, microbes and models: fundamental understanding of the soil methane cycle for future predictions
TL;DR: This work synthesizes recent knowledge on soil microbial and biogeochemical process and the impacts of climate change factors on the soil methane cycle to identify the source and magnitude of methane flux and the global factors that may change the flux rate and magnitude in the future.
Abstract: Methane is an important greenhouse gas and microbes in the environment play major roles in both global methane emissions and terrestrial sinks However, a full mechanistic understanding of the response of the methane cycle to global change is lacking Recent studies suggest that a number of biological and environmental processes can influence the net flux of methane from soils to the atmosphere but the magnitude and direction of their impact are still debated Here, we synthesize recent knowledge on soil microbial and biogeochemical process and the impacts of climate change factors on the soil methane cycle We focus on (i) identification of the source and magnitude of methane flux and the global factors that may change the flux rate and magnitude in the future, (ii) the microbial communities responsible for methane production and terrestrial sinks, and (iii) how they will respond to future climatic scenarios and the consequences for feedback responses at a global scale We also identify the research gaps in each of the topics identified above, provide evidence which can be used to demonstrate microbial regulation of methane cycle and suggest that incorporation of microbial data from emerging -omic technologies could be harnessed to increase the predictive power of simulation models
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TL;DR: It is argued that it is urgently necessary to incorporate microbial traits into biogeochemical ecosystem modeling in order to increase the estimation reliability of N2O emissions and proposed a molecular methodology oriented framework from gene to ecosystem scales for more robust prediction and mitigation of future N1O emissions.
Abstract: The continuous increase of the greenhouse gas nitrous oxide (N2O) in the atmosphere due to increasing anthropogenic nitrogen input in agriculture has become a global concern. In recent years, identification of the microbial assemblages responsible for soil N2O production has substantially advanced with the development of molecular technologies and the discoveries of novel functional guilds and new types of metabolism. However, few practical tools are available to effectively reduce in situ soil N2O flux. Combating the negative impacts of increasing N2O fluxes poses considerable challenges and will be ineffective without successfully incorporating microbially regulated N2O processes into ecosystem modeling and mitigation strategies. Here, we synthesize the latest knowledge of (i) the key microbial pathways regulating N2O production and consumption processes in terrestrial ecosystems and the critical environmental factors influencing their occurrence, and (ii) the relative contributions of major biological pathways to soil N2O emissions by analyzing available natural isotopic signatures of N2O and by using stable isotope enrichment and inhibition techniques. We argue that it is urgently necessary to incorporate microbial traits into biogeochemical ecosystem modeling in order to increase the estimation reliability of N2O emissions. We further propose a molecular methodology oriented framework from gene to ecosystem scales for more robust prediction and mitigation of future N2O emissions.
499 citations
Cites background from "Methane, microbes and models: funda..."
...and to improve the simulation performance in N2O modeling (Nazaries et al. 2013)....
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...…of N2O by specialized groups of functional organisms, aremore sensitive to changes inmicrobial community structure, and thus parameterization and incorporation of microbial data into models will have a great potential to improve their predictive power (Singh et al. 2010; Nazaries et al. 2013)....
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...…microelectrodes and open-path Fourier transform infrared (OP-FTIR) (Bai et al. 2014) will be essential to account for the temporal dynamics of microbes, to obtain robust field datasets for different ecosystem types and to improve the simulation performance in N2O modeling (Nazaries et al. 2013)....
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TL;DR: Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus, and mediate multiple critical steps in the nitrogen cycle, including N fixation.
Abstract: The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously.
380 citations
TL;DR: In this article, the authors synthesize biological, geochemical, and physically focused CH4 climate feedback literature, bringing together the key findings of these disciplines, and discuss environment-specific feedback processes, including the microbial, physical, and geochemical interlinkages and the timescales on which they operate.
Abstract: Methane (CH4) is produced in many natural systems that are vulnerable to change under a warming climate, yet current CH4 budgets, as well as future shifts in CH4 emissions, have high uncertainties. Climate change has the potential to increase CH4 emissions from critical systems such as wetlands, marine and freshwater systems, permafrost, and methane hydrates, through shifts in temperature, hydrology, vegetation, landscape disturbance, and sea level rise. Increased CH4 emissions from these systems would in turn induce further climate change, resulting in a positive climate feedback. Here we synthesize biological, geochemical, and physically focused CH4 climate feedback literature, bringing together the key findings of these disciplines. We discuss environment-specific feedback processes, including the microbial, physical, and geochemical interlinkages and the timescales on which they operate, and present the current state of knowledge of CH4 climate feedbacks in the immediate and distant future. The important linkages between microbial activity and climate warming are discussed with the aim to better constrain the sensitivity of the CH4 cycle to future climate predictions. We determine that wetlands will form the majority of the CH4 climate feedback up to 2100. Beyond this timescale, CH4 emissions from marine and freshwater systems and permafrost environments could become more important. Significant CH4 emissions to the atmosphere from the dissociation of methane hydrates are not expected in the near future. Our key findings highlight the importance of quantifying whether CH4 consumption can counterbalance CH4 production under future climate scenarios.
356 citations
Cites background from "Methane, microbes and models: funda..."
...In terrestrial zones, elevated atmospheric CO2 can increase primary production and organic C transfer to the rhizosphere (the soil zone influenced by microbial and plant root dynamics), increasing resource availability for methanogenesis (Figure 4) (Nazaries et al., 2013)....
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...Methanotrophy in these zones is thought to be less influenced by temperature and more by soil moisture, which controls oxygen availability (Nazaries et al., 2013)....
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TL;DR: It is argued that although making direct linkage of genomes to global phenomena is a significant challenge, many connections at intermediate scales are viable with integrated application of new systems biology approaches and powerful analytical and modelling techniques.
348 citations
TL;DR: This review summarizes the scarce available data on the exchange of VOCs between soil and atmosphere and the features of the soil and particle structure allowing diffusion of volatiles in the soil, which is the prerequisite for biological VOC-based interactions.
Abstract: Volatile compounds are usually associated with an appearance/presence in the atmosphere. Recent advances, however, indicated that the soil is a huge reservoir and source of biogenic volatile organic compounds (bVOCs), which are formed from decomposing litter and dead organic material or are synthesized by underground living organism or organs and tissues of plants. This review summarizes the scarce available data on the exchange of VOCs between soil and atmosphere and the features of the soil and particle structure allowing diffusion of volatiles in the soil, which is the prerequisite for biological VOC-based interactions. In fact, soil may function either as a sink or as a source of bVOCs. Soil VOC emissions to the atmosphere are often 1-2 (0-3) orders of magnitude lower than those from aboveground vegetation. Microorganisms and the plant root system are the major sources for bVOCs. The current methodology to detect belowground volatiles is described as well as the metabolic capabilities resulting in the wealth of microbial and root VOC emissions. Furthermore, VOC profiles are discussed as non-destructive fingerprints for the detection of organisms. In the last chapter, belowground volatile-based bi- and multi-trophic interactions between microorganisms, plants and invertebrates in the soil are discussed.
303 citations
Cites background from "Methane, microbes and models: funda..."
...Methane (CH4) is an important greenhouse gas, and microbes play major roles in both emission and uptake (Nazaries et al. 2013)....
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References
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01 Jan 2007
TL;DR: The first volume of the IPCC's Fourth Assessment Report as mentioned in this paper was published in 2007 and covers several topics including the extensive range of observations now available for the atmosphere and surface, changes in sea level, assesses the paleoclimatic perspective, climate change causes both natural and anthropogenic, and climate models for projections of global climate.
Abstract: This report is the first volume of the IPCC's Fourth Assessment Report. It covers several topics including the extensive range of observations now available for the atmosphere and surface, changes in sea level, assesses the paleoclimatic perspective, climate change causes both natural and anthropogenic, and climate models for projections of global climate.
32,826 citations
01 Jan 1997
TL;DR: This informal consolidated text of the Kyoto Protocol incorporates the Amendment adopted at the eighth session of the Conference of the Parties serving as the meeting of the parties to Kyoto Protocol (Doha Amendment).
Abstract: ____________________________________________ *This informal consolidated text of the Kyoto Protocol incorporates the Amendment adopted at the eighth session of the Conference of the Parties serving as the meeting of the Parties to the Kyoto Protocol (Doha Amendment). The Doha Amendment has not, as yet, entered into force. The informal consolidated text therefore has no official legal status and has been prepared by the secretariat solely to assist Parties. 1 KYOTO PROTOCOL TO THE UNITED NATIONS FRAMEWORK CONVENTION ON CLIMATE CHANGE*
5,435 citations
TL;DR: This work has suggested that several environmental constraints obscure the intrinsic temperature sensitivity of substrate decomposition, causing lower observed ‘apparent’ temperature sensitivity, and these constraints may, themselves, be sensitive to climate.
Abstract: Significantly more carbon is stored in the world's soils--including peatlands, wetlands and permafrost--than is present in the atmosphere. Disagreement exists, however, regarding the effects of climate change on global soil carbon stocks. If carbon stored belowground is transferred to the atmosphere by a warming-induced acceleration of its decomposition, a positive feedback to climate change would occur. Conversely, if increases of plant-derived carbon inputs to soils exceed increases in decomposition, the feedback would be negative. Despite much research, a consensus has not yet emerged on the temperature sensitivity of soil carbon decomposition. Unravelling the feedback effect is particularly difficult, because the diverse soil organic compounds exhibit a wide range of kinetic properties, which determine the intrinsic temperature sensitivity of their decomposition. Moreover, several environmental constraints obscure the intrinsic temperature sensitivity of substrate decomposition, causing lower observed 'apparent' temperature sensitivity, and these constraints may, themselves, be sensitive to climate.
5,367 citations
"Methane, microbes and models: funda..." refers background in this paper
...However, a consensus exists for these estimations by predictive models that need to incorporate biological processes and microbial communities (Davidson and Janssens, 2006; Singh et al., 2010)....
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TL;DR: In this article, the authors provide microscopic evidence for a structured consortium of archaea and sulphate-reducing bacteria, which are identified by fluorescence in situ hybridization using specific 16S rRNA-targeted oligonucleotide probes.
Abstract: A large fraction of globally produced methane is converted to CO2 by anaerobic oxidation in marine sediments. Strong geochemical evidence for net methane consumption in anoxic sediments is based on methane profiles, radiotracer experiments and stable carbon isotope data. But the elusive microorganisms mediating this reaction have not yet been isolated, and the pathway of anaerobic oxidation of methane is insufficiently understood. Recent data suggest that certain archaea reverse the process of methanogenesis by interaction with sulphate-reducing bacteria. Here we provide microscopic evidence for a structured consortium of archaea and sulphate-reducing bacteria, which we identified by fluorescence in situ hybridization using specific 16S rRNA-targeted oligonucleotide probes. In this example of a structured archaeal-bacterial symbiosis, the archaea grow in dense aggregates of about 100 cells and are surrounded by sulphate-reducing bacteria. These aggregates were abundant in gas-hydrate-rich sediments with extremely high rates of methane-based sulphate reduction, and apparently mediate anaerobic oxidation of methane.
2,679 citations
"Methane, microbes and models: funda..." refers background in this paper
...Anaerobic oxidation of methane (AOM) is carried out by a tight/physical association of anaerobic methanotrophic (ANME) Archaea and sulfate-reducing bacteria (SRB), Desulfosarcina and Desulfococcus of the Deltaproteobacteria class (Hinrichs et al., 1999; Boetius et al., 2000; Knittel and Boetius, 2009)....
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TL;DR: In this article, the anaerobic zones of submerged soils by methanogens and methanotrophs are oxidised into CO2 in the aerobic zones of wetland soils and in upland soils.
1,743 citations