Tree CH4 emissions are high in forested wetland and floodplain forests where tree trunks are viewed simply as pipes transferring CH4 produced in the soil and emitting it into the atmosphere. Trees in upland forests are also able to transfer CH4 from deep soil layers where anaerobic conditions prevail. In addition, CH4 that accumulates in living tree trunks can also be produced by methanogenic archaea in the wood if favourable environmental conditions for CH4 production prevail.
Inconsistent vertical patterns of trunk CH4 emission and internal CH4 concentrations are observed between species or between trees of the same species when CH4 is produced internally. Large radial variations in CH4 emissions is also observed, with for example hotspots located on one side of the tree. Furthermore, large variations in CH4 emissions and internal concentrations from year to year suggest temporal dynamics of methanogenic activity within hotspots. CH4 is the ultimate waste product of the energy metabolism of methanogens, which requires available substrates provided by a cascade of catabolic reactions breaking down macromolecules present in the wood. The inclusion of a biochemical module of CH4 production in physical models of CH4 transport within the trunk requires characterizing what shapes the environments favorable to CH4 production within the trunk, the biochemical processes producing upstream the substrates necessary for methanogenesis and the microbial communities involved in these processes.
The aim of this presentation is to review current knowledge on internal CH4 production and highlight challenges to build a comprehensive biogeochemistry of the trunk of living trees. Wetwood in living tree trunks is for example an ideal anoxic environment for methanogens, and this is where they were first found in the 1970s, but neither a necessary nor a sufficient condition. Methanogenic microbes in the trunk of living trees was recently found ubiquitous. However, the starting point of complex biogeochemical processes, supplying substrates and energy, but also inhibitors, to a unique microbiome in a unique ecological niche, is still not well understood.
How to cite: Epron, D., Mochidome, T., Cousteur, N., Plain, C., Watanabe, T., Nakada, R., and Asakawa, S.: What shapes the environments favorable to methane production in the trunks of living trees, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-4646, https://doi.org/10.5194/egusphere-egu25-4646, 2025.
The vegetation and soils of the Amazon contain substantial amounts of carbon, with a portion of this carbon decomposing into methane (CH4) under anaerobic conditions. A significant quantity of the resultant CH4 is released into the atmosphere through tree stems. Given large variations in landscape and vegetation across the Amazon region, there remains a gap in our understanding of the distribution and influence of CH4 cycling processes (e.g., production, oxidation and transport) in the soil/water-trees-atmosphere continuum of Amazonian forest ecosystems. Natural abundance stable isotopes are powerful tracers of these processes but their application in the Amazon has so far been limited.
In this study, we report the results of carbon and hydrogen isotopic compositions of CH4 in gas samples obtained from different sources (e.g., stem chambers, stem boreholes, bubbles, soil gases, etc.) collected during three intensive field campaigns (two dry seasons: August 2022, September 2023, one wet season: March-April 2023). These campaigns were conducted in two different forest ecosystems (Igapo: seasonally flooded blackwater forest, Baixio: upland swamp valley forest) around the Amazon Tall Tower Observatory (ATTO) site, located in the intact central Amazon region. We conducted stem chamber sampling on 6-7 tree species at each forest site and collected stem borehole gas samples from CH4 hotspot trees and palms (Igapo: Macrolobium acaciifolium and Pouteria elegans, Baixio: Mauritia flexuosa). We estimated the source isotopic signatures of stem CH4 emission using the Keeling plot method. In addition, based on the three different campaigns, we investigated seasonal and inter-site variations in stem CH4 isotopic composition and also dual isotope relationships (δ13C-CH4 vs. δ2H-CH4, δ13C-CH4 vs. δ13C-CO2) to trace CH4 cycling processes in the soil/water-tree-atmosphere continuum.
The carbon isotopic signatures (δ13C-CH4) of stem CH4 emissions at the Baixio site ranged from -90 ‰ to -45 ‰, whereas the Igapo site displayed a range between -70 ‰ and -20 ‰. The δ13C-CH4 values of stem CH4 emissions from CH4 hotspot trees at the Igapo site were approximately 5-10 ‰ lighter than those of stem-borehole and bubble samples. This isotopic difference was mostly consistent across three term campaigns, indicating that diffusive isotopic fractionation by stem CH4 emissions of these tree species remains constant across seasons. In contrast, the isotopic differences in δ13C-CH4 between stem CH4 emissions and stem-borehole samples from CH4 hotspot trees at the Baixio site were approximately 20 ‰, which is approximately two times higher than at the Igapo site. The dual isotope relationships indicate that methane of the stem interior is predominantly derived from acetate fermentation in the Baixio site, whereas CH4 oxidation generates stable carbon isotopic signatures of the stem interior in the Igapo site. This study provides valuable insights into CH4 processes within the soil/water-tree-atmosphere continuum in the central Amazon rainforest, which would contribute to improving our process understanding and thus prediction of Amazonian CH4 budgets.
How to cite: Komiya, S., Botia, S., van Asperen, H., Horna, V., Cunha, H. F. V., Schongart, J., Piedade, M. T. F., Wittmann, F., Marra, D. M., van der Veen, C., Rockmann, T., Trumbore, S., and Jones, S. P.: Stable isotopic characterization of CH4 emissions from tree stems in a central Amazon region , EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-21743, https://doi.org/10.5194/egusphere-egu25-21743, 2025.
Tropical wetlands are the largest natural source of methane (CH4) globally. While soils are the primary CH4 emitters, recent studies reveal that trees mediate soil-produced methane, highlighting potential underestimations in current methane and carbon budgets. In mangrove forests, the contribution of trees to local, regional, and global CH4 emissions remains uncertain, despite their significant role as blue carbon reservoirs. Mangrove species exhibit unique physiological and morpho-anatomical adaptations—such as extensive aerenchyma tissues and lenticels—that facilitate gas exchange through their bark and roots. In this study, we assessed the spatiotemporal variation of CH4 emissions from tree stems and stilt roots of three mangrove species (Rhizophora mangle, Avicennia germinans, and Laguncularia racemosa) across distinct ecological types (i.e., scrub, basin and hammock) during the rainy and dry seasons in the Ría Celestún Biosphere Reserve (Mexico). We also investigated the relationship between bark anatomical traits, aerenchyma development, and CH4 fluxes. Our findings revealed that CH4 emissions varied by species, tissue type, and season. Scrub R. mangle showed the highest CH4 emission rates from both tree stems and stilt roots, particularly in near-ground tissues like third-order stilt roots with abundant bark aerenchyma, whereas basin mangrove forests had the lowest emissions, particularly in A. germinans and L. racemosa. Methane emissions increased during the rainy season and were positively correlated with bark (aerenchyma) proportion, lenticel density but negatively with wood density. To date, tree stem CH4 emissions have been documented in eleven mangrove species globally. Our results underscore the need to refine local-to-global carbon models by integrating bark anatomy and tree-mediated CH4 emissions. Moreover, mangrove trees can act as either CH4 sources or sinks, depending on physicochemical and microenvironmental conditions. Understanding these dynamics requires a comprehensive approach rooted in plant physiology and anatomy.
How to cite: Salas Rabaza, J. A., Thalasso, F., Yáñez Espinosa, L., Cejudo, E., Pangala, S. R., Cerón Aguilera, G., Us Santamaría, R., and Andrade, J. L.: The bark side of mangrove methane fluxes: Anatomical insights of the root of emissions in Rhizophora forests, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-11389, https://doi.org/10.5194/egusphere-egu25-11389, 2025.
Trees, typically large trees in upland forests, emit CH4 produced in their trunk by methanogenic archaea. In this case, spatial variability of emission can be more complicated than when tree trunks act as a passive conduit for CH4 produced in the soil. However, due to poor accessibility, CH4 emissions from the trunk above 3 m, where a researcher cannot reach without a ladder, scaffold or crane, have not been well studied. The vertical emission patterns from trunks, including the upper part, and the processes driving them, i.e., CH4 production and transport, remain unexplored.
Using a crane truck, we investigated vertical patterns of CH4 emissions, internal CH4 concentration and production up to 12 m above ground in six trees of three species in a cool-temperate upland forest. We also conducted a modelling study of CH4 transport within trunks to know whether CH4 emitted from the upper part of the trunk, if present, is produced locally at the same height of the trunk or is produced elsewhere and transported to that height.
CH4 was actively emitted from the trunk at a height greater than 3 m, with peak emissions at 4 to 6 m above ground in some trees. CH4 production was observed consistently up to the highest sampling point at 12 m height. CH4 production hotspots in Japanese beech and horse-chestnut trees were characterized as decaying wood due to their low density and high moisture content. In Japanese cedar, production hotspots were surrounded by wet sapwood, suggesting that limited oxygen diffusion to the tree centre stimulated CH4 production. According to CH4 transport modelling, axial CH4 transport from the production hotspot upwards is more likely in trees with low radial diffusion. However, within a realistic parameter range, such long-distance axial CH4 transport could not be realized.
The results highlighted the complexity of endogenously produced CH4 emissions in the trunk. Oxygen level and wood decay, as suggested by our results, could be key factors to explain the heterogeneity of CH4 production inside the trunk, which can efficiently predict the spatial variability of the emission along the trunk height.
How to cite: Mochidome, T., Hölttä, T., Dannoura, M., and Epron, D.: Significant CH4 production and emission in the upper part of the tree trunk, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-14314, https://doi.org/10.5194/egusphere-egu25-14314, 2025.
Methane (CH4) is the second most significant anthropogenic greenhouse gas after CO2, contributing to 20% of global warming. Low CH4 emission by stems in well-aerated forest soils can influence global carbon cycles, mainly by reducing the CH4 sink capacity of forests. Methane could be produced in anoxic soil zones, mainly when soil water is high, from late autumn to early spring. Methanogenesis occurs not only in soil since methanogenic archaea have been identified in the heartwood of trees where high concentrations of CH4 were recorded. However, these concentrations do not lead directly to high emissions, as the CH4 can be oxidised by the communities of methanotrophs also present in the tree and/or transported elsewhere.
To explore seasonal variations in methane fluxes (FCH4) and the factors involved, methane fluxes were manually recorded 13 times at four heights (0.5, 1.3, 2 and 4 m) on the stems of three common temperate tree species (Carpinus betulus, Fagus sylvatica, and Quercus robur) in the Hesse forest (ICOS site, NE of France) from April 2023 to March 2024, using a trace gas analyser. The three species at this site have different root depth profiles, with the root system of Q. robur being deeper.
Over the sampling period, tree were low methane emitters for all species (mean ± SE, 0.71 ± 0.34 µg CH₄ h⁻¹), with notable variability, particularly for Q. robur, ranging from - 12.47 to 15.64 µg CH₄ h⁻¹. Methane fluxes especially below 1.5 meters varied along the year in relation to the 3 levels in soil moisture defined according to the water table level (wet: water table above 0.55 m, dry: water table below 1 m and moderate: intermediate and the two above). Methane emitted by the three species differed with soil moisture. Q. robur exhibited lower emissions only during driest soil conditions, as its deep root system allows access to methane production zones deeper in the soil. In contrast, F. sylvatica showed reduced emissions at both drier (moderate and dry) levels, likely due to its shallower root system's limiting access to methane-rich soil layers.But methane emissions did not decrease with height or with decreasing soil water content in all trees, indicating that methane could be produced inside the wood. In fact, in one third of the wood cores sampled, potential methanogenic production was recorded.
Our study confirmed that methane emissions from trees are influenced both by soil methane and by internal production processes. Our work has shown that the differences in emissions between species could be explained by the root profile.
How to cite: Cousteur, N., Courtois, P., Joetzjer, E., and Plain, C.: In a well-aerated temperate forest soil, the response of stem methane emissions to variations in soil water content depends on the tree species and stem height measured, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-19813, https://doi.org/10.5194/egusphere-egu25-19813, 2025.
Coastal ecosystems are highly vulnerable to climate change due to sea level rise, increased storm frequency and intensity, and changes in precipitation patterns. These hydrological disturbances affect soil biogeochemical processes in coastal forests, potentially transforming these upland habitats into wetlands and changing ecological functions. However, the initial impacts on belowground processes and the mechanisms driving GHG fluxes during this transition remain poorly understood. This study investigates how flooding events with different water chemistries influence the production and consumption of GHGs in coastal forest soils under controlled laboratory conditions. Intact soil cores were collected from a temperate deciduous coastal forest in Maryland, USA. Freshwater (FW) and brackish water (BW) pulses were applied to simulate intense rainfall and storm surge events, respectively. Continuous CO2, CH4, and N2O emissions were measured and coupled with air isotopic sampling (δ13C-CO2, δ13C-CH4) and porewater chemistry analyses (DOC, S2-, Fe2+, Fe3+, Mn2+, NH3, NO3-+NO2-, ORP, pH) to identify potential changes in metabolic pathways and characterize the biogeochemical responses. The results underscore the impact of water chemistry on biogeochemical processes, particularly in the BW treatment, which exhibited strong reducing conditions and active microbial metabolism. The elevated salinity and sulfate concentrations were associated with increased emissions of CH4 and N2O. The δ13C-CH4 signature and elevated S2- in porewater indicated the co-occurrence of methylotrophic methanogenesis and sulfate reduction. Elevated NH3 concentrations and NO3-+NO2- production suggested the potential occurrence of dissimilatory nitrate reduction to ammonium (DNRA) and incomplete denitrification. These findings highlight the potential vulnerability of upland coastal forest soils to hydrologic disturbances and the complex interactions involved in the response of these ecosystems to inundation stressors.
How to cite: Cruz, R., Bond-Lamberty, B., Montgomery, A., Pennington, S., Seyfferth, A., Wilson, S., and Vargas, R.: Flooding and Water Chemistry Drive Soil Biogeochemistry and GHG fluxes in a Coastal Forest , EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-10193, https://doi.org/10.5194/egusphere-egu25-10193, 2025.
Trees contribute to methane (CH₄) cycling through internal microbial processes and transport, with tree-mediated CH₄ emissions documented across various forest types, including upland ecosystems where soils typically act as CH₄ sinks. To investigate the microbial drivers of these emissions, we measured CH₄ fluxes from tree stems and surrounding soils across upland, intermediate, and wetland sites at Yale-Myers Forest, Connecticut, USA. While upland soils consistently consumed CH₄, tree stems emitted CH₄ at all landscape positions. Fluxes from upland tree stems showed no height-dependent decline, indicating internal methane production rather than soil-to-stem transport. Using droplet digital PCR (ddPCR) to quantify the mcrA gene, methanogen abundance in heartwood was over two orders of magnitude higher than in surrounding soils, with copy numbers ranging from 10⁴ to 10⁵ g⁻¹ in tree tissues compared to 10¹ to 10² g⁻¹ in soils.
Microbial sequencing revealed distinct methanogenic communities, including Methanobacterium and Methanomassiliicoccus, indicating primarily hydrogenotrophic pathways of methane production. Functional inference showed that methanogenesis pathways strongly correlated with fermentation pathways, including those producing hydrogen and acetate, suggesting syntrophic interactions between fermentative bacteria and methanogens. In contrast, methanogenesis pathways were anticorrelated with aerobic respiration and sulfur metabolism, indicating redox conditions suppress methane production in outer tissues. These findings emphasize that heartwood serves as a niche for anaerobic processes driving CH₄ production.
The internal tree microbiome was highly partitioned between tissues. Heartwood and sapwood microbiomes showed distinct microbial compositions and minimal similarity to surrounding soil communities. Heartwood was dominated by anaerobic bacteria and archaea, while sapwood and bark harbored methanotroph-related genes (pmoA, mmoX), indicating potential internal methane oxidation.
Internal gas sampling confirmed elevated CH₄ concentrations within stems, particularly at mid-stem heights, corresponding with visible heartwood decay. Methanotroph-related genes detected in sapwood and bark suggest some gross methane oxidation, but methanogenesis pathways dominated, resulting in net positive fluxes from tree stem to atmosphere. These findings underscore tree microbiomes' importance in methane cycling, with heartwood providing an anaerobic niche for microbial methane metabolism in upland forests.
How to cite: Gewirtzman, J., Arnold, W., Raymond, P., Peccia, J., and Bradford, M.: Species and Tissue-Specific Microbiomes Drive Methane Fluxes from Trees, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-14365, https://doi.org/10.5194/egusphere-egu25-14365, 2025.
Microbes are the key players in the global cycling of nitrogen (N) and carbon (C), controlling the availability and fluxes of C and N in ecosystems, as well as being responsible for losses through the emissions of the powerful greenhouse gasses nitrous oxide (N2O) and methane (CH4). Thus, characterization of microbial functional guilds involved in these processes is high on the scientific agenda. Yet, standard sequence-based characterization methods often reveal only a minor fraction of their diversity in nature due to their frequent low relative abundance, insufficient sequencing depth of traditional metagenomes of complex communities, and limitations in coverage and efficiency of PCR-based assays.
Here, we developed and tested a targeted metagenomic approach based on probe capture and hybridization to simultaneously characterize the diversity of multiple key metabolic genes involved in inorganic N and CH4 cycling. We designed comprehensive probe libraries for each of 14 target marker genes, comprising 264,000 unique probes in total. These probes were used to selectively enrich the target genes in shotgun metagenomic libraries.
In validation experiments with mock communities of cultured microorganisms, the target gene profiles were similar to those of the original community when sequenced with targeted metagenomics. Furthermore, relative abundances of the marker genes obtained by targeted and shotgun metagenomics from agricultural and wetland soils correlated positively, indicating that the targeted approach did not introduce a significant quantitative bias. However, targeted metagenomics generated substantially higher diversity in terms of taxonomic coverage, and a larger number of sequence reads per sample, which allowed 28 or 1.24 times higher diversity estimates than when using shotgun metagenomics or targeted PCR amplification, respectively.
The targeted metagenomics tool has been used to study the nitrogen and methane cycling microbes successfully in tropical corals for N cyclers (Glaze et al. 2022) and boreal spruce phyllosphere tissues for methane cyclers (Putkinen et al. 2021). However, the role of the CH4 and N2O cycling microbes within the plant and lichen tissues are still relatively unknow. The results of gas dynamics, isotopic labelling and targeted metagenomic results in the plant tissues will be discussed. In summary, targeted metagenomics complements current approaches by enabling a targeted, more detailed characterization of the diversity (Siljanen et al. 2024) of key functional genes involved in N and CH4 cycling within and between ecosystems.
REFERENCES
Glaze T.D., Erler D.V., Siljanen H. (2022). Microbially facilitated nitrogen cycling processes in tropical corals. ISME Journal. 16:68-77. https://doi.org/10.1038/s41396-021-01038-1
Putkinen A., Siljanen H.M.P., Laihonen A., Paasisalo I., Porkka K., Tiirola M., Pihlatie M. (2021). New insight to the role of microbes in the methane exchange in trees: evidence from metagenomic sequencing. New Phytol. 231: 524-536
Siljanen H.M.P, Manoharan L., Hilts A.S., Bagnoud A., Alves R.J.E., Jones C.M., Kerous M., Sousa F.L., Hallin S., Biasi C., Schleper C. (2024). Targeted metagenomics using probe capture detects a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics bioRxiv, https://doi.org/10.1101/2022.11.04.515048
How to cite: Siljanen, H. M. P., Manoharan, L., Hilts, A., Bagnoud, A., Alves, R. J. E., Jones, C. M., Kerou, M., Kerttula, J., Thiyagarasaiyar, K., Abagnale, V., Soosaar, K., Mander, Ü., Machácová, K., Pumpanen, J., Palacin-Lizarbe, C., Paul, D., Sousa, F. L., Hallin, S., Biasi, C., and Schleper, C.: Targeted metagenomics using probe capture detects a larger diversity of nitrogen and methane cycling genes than traditional metagenomics – can microbes cause an ecosystem services in the plant tissues?, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-19642, https://doi.org/10.5194/egusphere-egu25-19642, 2025.
Posters on site: Wed, 30 Apr, 14:00–15:45 | Hall X1
Globally, tropical forests are thought to be an important source of atmospheric nitrous oxide (N2O) and a sink for methane (CH4), with small biome-wide changes in the structure, dynamics and environment of these forests either mitigating or exacerbating increases in atmospheric concentrations of these major greenhouse gases (GHGs). Anthropogenic activities have dramatically increased nitrogen (N) and phosphorus (P) inputs to the biosphere, potentially altering soil biogeochemical cycles. However, the effects of N and P addition on soil CH4 and N2O fluxes in tropical forest ecosystems are not yet understood. Besides soils, tree-mediated transport can also contribute significantly to GHG exchange in forests. In the soil, CH4 and N2O produced can be absorbed by roots and transported into aboveground tree tissues. In addition, these gases can be produced in trees by microorganisms living in the tissues or by physiological and photochemical processes. Yet observations of CH4 and N2O fluxes in tropical forests, particularly in tree stems, are still limited and have not been described in the context of long-term nutrient addition experiments.
Here we report data derived from measurements of soil and stem fluxes and environmental variables in N (+N) and P (+P) addition plots over seven years in a tropical forest of the north-eastern Amazon, French Guiana. In each plot (+N, +P, +NP and controls), CH4 and N2O fluxes, soil water content (SWC), soil and air temperature, total N and carbon content and available P were measured at five different locations combining a tree stem (> 30 cm diameter) and its surrounding soil. These measurements were made in plots located in three contrasting habitats, a well-drained, nutrient-poor soil at the top of the hill (upland area) and two waterlogged, nutrient-rich soils at the bottom of the hill (seasonally and permanently flooded areas).
We found that soil and stem CH4 and N2O fluxes were highly spatially variable in situ. In the control plots, soil CH4 uptake and N2O emissions decreased with increasing SWC (i.e. from the hill-top to the wettest hill-bottom). Regardless of the forest habitat, N additions (+N and +NP) resulted in substantially higher soil N2O fluxes, whereas P additions (+P) resulted almost exclusively in soil CH4 uptake. This suggests that N addition increases soil N beyond microbial immobilisation and plant nutritional requirements, with the excess being nitrified or denitrified, while P addition stimulates soil methanotrophic activity. In the control plots, stems growing in the waterlogged soils of the permanently flooded area were moderate and strong emitters of N2O and CH4, respectively. For both gases, CH4 and N2O, higher stem fluxes resulted from P addition (+P and +NP) in hill-bottom plots.
Our results highlight (i) the key role of N and P in CH4 and N2O cycling in tropical forest soils and (ii) the substantial CH4 and N2O source potential of tree stems in highly waterlogged areas. This underlines the importance of including processes related to water, N and P availability in GHG flux modelling in tropical forests.
How to cite: Bréchet, L., Macháčová, K., Klem, K., and Medňanský, T.: Long-term nitrogen and phosphorus additions alter soil and tree stem methane and nitrous oxide fluxes under contrasting soil water conditions in a tropical forest, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-12762, https://doi.org/10.5194/egusphere-egu25-12762, 2025.
This study is part of an international mission in the Amazon rainforest, involving researchers from the Federal University of Rio de Janeiro, Universities of Leeds, Linköping, British Columbia, and coordinated by Prof. Vincent Gauci and Dr. Sunitha Pangala. The primary objective is to reconcile top-down methane (CH₄) emission estimates, derived from remote sensing data over Amazon floodplains, with bottom-up measurements obtained from field studies. Previous satellite observations indicated a discrepancy of 20 million tons of CH₄ emitted annually, a significant gap that could not be fully explained by ground-based sources. This project aimed to resolve this difference by integrating both remote sensing satellites and field data using ABB’s Off-Axis Integrated Cavity Output Spectroscopy (OA-ICOS) to understand and bring to light the different dynamics involved in methane emissions in the Amazon rainforest.
Reconciling top-down and bottom-up carbon budgets can be particularly challenging in specific ecosystems where topography complicates site access and sampling. Under such conditions, the availability of compact and rugged cavity-enhanced laser-based analyzers offering sub-ppb precision is invaluable for environmental scientists. ABB’s portable greenhouse gas ultraportable analyser, GLA132-GGA (47 cm × 35.56 cm × 17.78 cm) is capable of monitoring CH4 with a 1 s precision of 1.4 ppb, which can be improved to 0.2 ppb with 100 s averaging time. The analyser is based on OA-ICOS technology that combines high precision capabilities through enhanced cavity path length and robustness to mechanical vibrations, which is crucial to field applications. Scientists used semi-rigid custom chambers wrapped around the trunk of floodplain trees and connected them to the GLA132-GGA to measure individual CH4 emissions from 2357 trees in 13 floodplain sites.
The findings provide a crucial link to reconcile the 20-million-ton discrepancy in Amazon's methane budget. Scaled estimates of methane flux emitted from floodplain trees align closely with the missing methane observed in previous satellite data. During the rainy season, when Amazon tree roots become submerged, trees have evolved specialized adaptations to enhance oxygen supply to their roots by enlarging pores in their stems. This adaptation inadvertently facilitates the release of methane, produced by microorganisms in the waterlogged soil, through the same pore openings. Floodplain trees thus function as natural chimneys, venting substantial quantities of methane into the atmosphere. These large emissions from floodplain trees play a pivotal role in closing the Amazon methane budget.
Furthermore, a second campaign revealed that methane produced deep within the soil column can also escape to the atmosphere via tree roots, even when the water table is below the surface. Regression analysis demonstrated that, while methane emissions show negligible response to increased flood levels above the soil surface, there is a clear dependence of whole-tree methane emissions on the presence of submerged roots. This highlights the importance of floodplain trees in regulating methane fluxes across varying hydrological conditions, underscoring their significant role in the global methane cycle.
How to cite: Nataraj, A., Despagne, F., Owen, K., Lobo Neto, J., and Baer, D.: Bridging the Gap: Integrating Top-Down and Bottom-Up Measurement Approaches to close the Amazon CH4 emissions budget , EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-14261, https://doi.org/10.5194/egusphere-egu25-14261, 2025.
Peatland cloud forests represent one of the least studied ecosystems regarding methane (CH4) exchange despite their significance in carbon storage and the highly variable soil moisture that results from the presence of clouds in these environments. We aimed to investigate the CH4 exchange in the peat soil and tree stems of two selected tropical cloud forests on Réunion Island (one featuring Erica reunionensis and a second mix of E. reunionensis and Alsophila glaucifolia). Additionally, we explored the soil microbiology in various below- and above-ground forest compartments (soil, canopy soil, leaves, and stems) by exploring gene abundances and the microbial community structure.
In this study, we measured CH4 fluxes from peat soil and tree stems using GC-ECD and LI-COR LI-7810 analyzers, respectively. Additionally, we performed metagenomics and qPCR on selected genes involved in methanogenesis and methanotrophy in the soil and above-ground samples. Soil’s physical and chemical properties were also determined.
The peat soil found in both forests functioned as a net sink for CH4 and a source of CO2, with increased CH4 uptake occurring in soils dominated by endemic tree species E. reunionensis. Additionally, the stems of trees in the mixed forest sites acted as a weak sink for CH4. In these soils, a high abundance of NC10 bacteria (involved in n-DAMO - nitrite/nitrate-dependent anaerobic methane oxidation) was associated with the high soil nitrate (NO3-) levels, CH4 sink values, and CO2 emissions, indicating a high potential for nitrate-dependent oxidation of CH4. The ratio of mcrA (methanogenesis) to pmoA and n-DAMO (methanotrophy) genes was consistently less than 1 in the soil of both forests, whereas it exceeded 1 in the above-ground samples, including cryptogamic canopy soils and tree leaves. Metagenomic analyses revealed that soil had a high prevalence of the xoxF gene, which is associated with n-DAMO, while the above-ground compartments of both forests exhibited a high abundance of methanogenic genes (mcrA and mtr).
The peat soil of tropical cloud forests exhibited a high potential for methanotrophy, with significant CH4 consumption by n-DAMO microbes. In contrast, the above-ground components of these forests may play a notable role in methanogenesis, occurring within cryptogams and leaves, as suggested by the high abundance of mcrA and mtr genes in the leaves and canopy soil.
How to cite: Kazmi, F. A., Mander, Ü., Khanongnuch, R., Öpik, M., Ranniku, R., Soosaar, K., Masta, M., Tenhovirta, S., Kasak, K., Ah-Peng, C., and Espenberg, M.: Distinct microbial communities drive the CH4 cycles in below and above-ground compartments of tropical peatland cloud forests , EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-6606, https://doi.org/10.5194/egusphere-egu25-6606, 2025.
Mangrove forest is one of the most carbon storing tropical forests. Thus, understanding the dynamics of greenhouse gas such as CO2 and CH4 are important to predict the future. CO2 is produced by plant respiration, dissolved in water and transported upwards with transpiration. Active respiration in mangrove roots occurs because salt from seawater must be excluded before water enters the xylem. Therefore, tidal fluctuation can affect the exchange of CO2 between tree surface and the atmosphere. CH4 is produced in anaerobic conditions in the sediment and is not readily soluble in water. However, it can diffuse through aerenchyma and pores in root and stem tissues, particularly during the day when the water potential becomes low and tissue air porosity increases. Because CH4 has a global warming potential that is 25 times more powerful than CO2 over 100 years, CH4 emissions have the potential to offset a part of the CO2 initially removed from the atmosphere by photosynthesis and buried as blue carbon in the sediment. Thus, both CO2 and CH4 fluxes should be considered in the carbon budget of mangrove ecosystems. The aim of this study was to determine how tidal and diurnal cycles affect CO2 and CH4 emissions from mangrove roots and stems, both physiologically and physically, for a more accurate understanding of gas exchange processes in mangrove forests.
The research was conducted on Bruguiera gymnorrhiza and Rhizophora stylosa on the bank of the Miyara River in Ishigaki island. Chambers were placed at three heights along the stems (approximately 0.2, 1.0, and 1.5 m above the sediment) and on different root types to measure CO2 and CH4 fluxes during day and night and low and high tide in June, August and November 2024.
CO2 efflux from the trunk showed no difference with height. In contrast, CH4 efflux was highest at the base of the trunks. At low tide, CH4 emissions from the roots were much higher than those from the trunk. Both CO2 and CH4 efflux from the trunk surface was lower at night than during the day, and there was no difference between high and low tide. Large variations in CH4 efflux was observed from the same position at different times. Continuous measurements are needed to better characterize these temporal variations. Characterizing the spatial distribution of roots is also a future challenge.
How to cite: Dannoura, M., Paul, S. K., Hredoy, R. R., Suwa, R., Tokito, M., and Epron, D.: Effect of tidal cycles on greenhouse gas emissions from mangroves, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-14176, https://doi.org/10.5194/egusphere-egu25-14176, 2025.
Upland trees can exchange CH4 with the atmosphere through the stems. Stem emissions could be produced in the soils and transported through the roots, or could be produced in the hardwood by methanogenic archaea inhabiting the trees. However, there is still limited information on how the different origins depend on different species or environmental conditions. There is the general understanding that stem CH4 emissions are controlled by soil moisture conditions, and therefore, trees from water-limited ecosystems might present little (if any) emissions. However, this hypothesis has not been tested yet in water-limited ecosystems, such as Mediterranean ones. Here we present a study on stem CH4 emissions from cork oak (Quercus suber), a drought-adapted species from the Mediterranean basin. The bark of this species (cork) is commonly extracted for business, since it has insulation characteristics. We assessed the effect of cork removal (peeling) on stem emissions, since cork may act as a physical barrier for methane diffusion from the stem to the atmosphere.
We measured CH4 stem emissions from peeled and unpeeled trees at two stem heights, one on the cork extraction zone (bottom part of the stem) and the other above it (unpeeled zone). Additionally, we performed wood anaerobic incubations to assess the CH4 production capacity, and analysed the microbial community composition in the hardwood, sapwood and cork tissues.
Our results showed that cork oaks emitted high CH4 rates (59.83 μmol m-2h-1 on average), which were positively correlated with DBH. Surprisingly, we did not see any effect of cork peeling in CH4 emissions, not even in the measurements performed immediately after the cork removal. We observed, however, a strong vertical pattern for all trees and campaigns, with emissions being higher on the base of the trees. Despite this vertical pattern, usually associated with soil CH4 origin, significant CH4 production in the tree cores, and a positive correlation between stem CH4 fluxes and the abundance of methanogenic-related genes suggest an internal stem origin of CH4. These results suggest that stem internal conditions might be more important controlling stem CH4 emissions than soil or atmospheric environmental conditions.
How to cite: Barba, J., Fíguls, R., Trullols, J. M., Bañeras, L., Gauci, V., Llorens, L., Pacheco, A., and Verdaguer, D.: Methane emissions and production from tree stems of Quercus suber in a Mediterranean forest, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-7346, https://doi.org/10.5194/egusphere-egu25-7346, 2025.
Floodplain forests play an important role in the exchange of methane (CH4) with the atmosphere. However, due to climate change and anthropogenic activities, main factors driving this exchange, such as ground water table and soil temperature, are constantly changing. The studied floodplain forest in Lanžhot, Czech Republic, represents nowadays relatively dry conditions.
The main aims of our study were to quantify the CH4 emission on the floodplain forest ecosystem level using the eddy covariance (EC) method, with special emphasis on environmental conditions, turbulence development and footprint, as well as to probe all potential CH4 sinks and sources within the studied ecosystem for arriving at a complete CH4 budget. The ecosystem-scale CH4 fluxes were analysed with regards to the CH4 emissions of water bodies within the EC footprint. For this purpose, 17 chamber measurements were conducted on the waterbodies every two weeks for two weeks periods and EC data were divided into such subperiods accordingly. CH4 fluxes from a stream located within the footprint of the EC tower were measured using floating chambers and bubble traps. Studies were complemented by the analysis of the contribution of trees to the CH4 exchange. For this purpose, stem chambers measured CH4 fluxes on hornbeam trees, one of the main tree species at the study site and in Central Europe. Additionally, CH4 fluxes from the soil were included in the analysis to capture all potential CH4 sources and sinks within the studied ecosystem.
We initially hypothesized that ecosystem-scale CH4 exchange will be negligible. Our results showed, however, that the whole ecosystem is a small but constant CH4 source as we observed an average emission flux of 11.7 mg CH4 m-2 day-1 over the period May 2022 – May 2023. In addition, we observed variability of the CH4 fluxes in relation to the wind direction and to u* (friction velocity, indicator for turbulence development). Further analysis shall answer on the question if more water bodies within a particular wind sector means higher fluxes above the canopy and if higher turbulence is correlated with higher CH4 fluxes above canopy as hotspot emissions are better mixed up. The probed stream was a substantial source of CH4 with median total CH4 flux = 156 mg CH4 m-2 day-1 from April 2022 to May 2023. Ebullition was the dominant pathway of CH4 release throughout the whole monitored period. The relation of water area/footprint area (%) of 17 floating chamber measurements ranged from 3 to 6% and fluxes coming from water bodies contributed to the EC fluxes significantly. From 17 subperiods, 15 of them were characterised by higher EC fluxes than fluxes coming from the water bodies. Two periods showed opposite result, which might indicate on additional sources of methane.
Finally, two models were applied to compare gapfilled data and answer on the question how the methane budget changes if we use different models.
The overall aim of this project is to arrive at a complete picture of all measured sinks and sources of CH4 in the studied ecosystem.
How to cite: Kowalska, N., Jocher, G., Bednařík, A., Warlo, H., Soosaar, K., and Macháčová, K.: Ecosystem-scale floodplain forest methane exchange , EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-5621, https://doi.org/10.5194/egusphere-egu25-5621, 2025.
Trees are known to be methane (CH4) sources and sinks. However, frequently observed large spatial variability in stem CH4 fluxes makes the estimation of net forest ecosystem CH4 exchange difficult. This variability refers not only to large intraspecies variability, but also to variability across vertical stem profiles.
European beech (Fagus sylvatica) is a native and widely grown tree species in upland forests of Central and Southeast Europe. Our previous study detected high spatial variability in stem CH4 emissions among twenty beech trees, which could not be explained by soil CH4 turnover.
We aimed to investigate whether the high variability in beech stem CH4 emissions can be explained by CH4 production and consumption in the studied trees’ stem wood. In August-September 2024, we measured CH4 exchange of eleven mature beech individuals (0.4 m above ground) and of adjacent soil in a temperate montane forest of White Carpathians, Czech Republic, using static chamber systems and spectroscopic gas analysis (FTIR technology). By five trees, stem CH4 fluxes were additionally measured along vertical stem profiles up to 2 m above ground (i.e. in three heights). The measurements were followed by wood core sampling in these profiles for further investigation of potential for CH4 production through methanogenesis and consumption through methanotrophy using incubation of wood samples.
The stem CH4 exchange showed large variation, ranging from CH4 uptake to CH4 emission (from -14.0 to +279 μg CH4 m-2 h-1), whereas the soil was a net CH4 sink with less variation (-41.4 ± 3.5 μg CH4 m-2 h-1). Fourteen days of incubation showed CH4 production in 34% of total tested wood cores. These cores originated from individuals and stem heights with increased CH4 emissions. The net incubation bottle headspace increase of CH4 was linear (R² > 0.7) with values of 0.1 ± 0.02 μg CH4 cm-3 h-1. During 25 days of incubation under anoxic conditions with labelled ¹³C-CH4 in the headspace, the increase in 45CO2/44CO2 ratio was used to monitor oxidation of labelled CH4. Significant net increase in this ratio was detected in several bottles. Interestingly, wood cores with the highest methanogenesis rates showed also faster increase in 45CO2/44CO2 ratio (p<0.001). This suggests that high CH4 production rates in these cores positively influence the community of methanotrophs which are either more abundant and/or more active in these cores. Whether methanotrophic community is represented by anaerobic methanotrophic archaea or by aerobic methanotrophs adapted to hypoxic conditions will be assessed by DNA analysis. Statistical analysis will investigate the relationships between CH4 fluxes, production and consumption to determine the fate of tree-derived CH4, a significant greenhouse gas.
Acknowledgement
This research was supported by the Ministry of Education, Youth and Sports of CR within the programs LU - INTER-EXCELLENCE II [LUC23162] and CzeCOS [LM2023048], and project AdAgriF -Advanced methods of greenhouse gases emission reduction and sequestration in agriculture and forest landscape for climate change mitigation [CZ.02.01.01/00/22_008/0004635]. VT was supported by the Czech Science Foundation (23-07434O).
How to cite: Machacova, K., Tláskal, V., Medňanský, T., Warlo, H., and Klem, K.: Does stem wood methanogenic and methanotrophic activity drive spatial patterns in methane emissions of mature European beech?, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-9586, https://doi.org/10.5194/egusphere-egu25-9586, 2025.
Forest soils play a critical role in the global methane (CH4) budget, but the magnitude of CH4 fluxes varies significantly across a landscape, spatially and temporally. In complex landscapes, soil hydrology is strongly influenced by variations in topography and vegetation, which affect soil CH4 fluxes (FCH4). Consequently, accurately scaling FCH4 to the landscape level is a significant challenge. This study aimed to develop a methodology for scaling seasonal FCH4 across a topographically complex landscape in a cold temperate mountain forest.
This study was conducted in the upper watershed of the Yura River in the Ashiu Experimental Forest (area 40 ha and elevation 600-850 m). The landscape was classified into upland, wetland, and river, comprising approximately 94%, 1%, and 5% of the total study area, respectively. 52 collars were installed in upland areas covering different topographic positions and vegetation types, and FCH4 were measured nine times from April to November. Additionally, 11 collars were installed in small riparian wetlands and measured twice during the wet-to-dry summer transition. Then, we used measured FCH4 together with topographic attributes i.e., slope, aspect, profile curvature (PRC), vertical distance to the channel network (VDCN), topographic position index (TPI), and topographic wetness index (TWI) from remotely sensed data (digital elevation model) and vegetation type (broadleaf, coniferous, and mixed) to develop a machine-learning model (quantile regression forest) for predicting upland seasonal FCH4 at 5 m resolution with uncertainty across the landscape level. A simple average was used to estimate the wetland fluxes.
Seven predictor variables were used to model upland FCH4 for each season; the selected predictors and model accuracy varied with seasons. The model accuracy was high in early autumn (R2 = 0.67) and low in early wet summer (R2 = 0.28). TPI was consistently selected in all seasons, while TWI was chosen for most seasons except two, where VDCN was selected instead. VDCN and PRC were occasionally selected with TWI and TPI. Vegetation type was not selected for any of the seasons. Across the landscape, predicted upland median seasonal FCH4 ranged from -0.35 to -0.60 g CH4 hr-1 ha-1 in spring, -0.41 to -1.25 g CH4 hr-1 ha-1 in summer, and -0.50 to -0.89 g CH4 hr-1 ha-1 in autumn. This seasonal variation in upland predicted median FCH4 was well explained by the antecedent precipitation index (R2 = 0.71, p < 0.01) calculated over 20 days. When scaled at the landscape level, the average CH4 uptake by upland soils was -25.1 (uncertainty -35.8 to -16.2) g CH4 hr-1. In the wet summer, small wetland patches offset 8% of the upland CH4 uptake (-15.6 g CH4 hr-1 upland, 1.2 g CH4 hr-1 wetland), and the following dry summer, they offset only 2% because both the upland CH4 uptake increased and the wetland emission decreased (-32.6 g CH4 hr⁻¹ upland, 0.5 g CH4 hr⁻¹ wetland). This study highlighted the efficiency of remote sensing and machine learning approaches to extrapolate field measurements to the landscape level and allowed us to visualize spatial patterns of fluxes over time.
How to cite: Paul, S. K., Epron, D., Yuasa, K., and Dannoura, M.: Scaling soil methane fluxes across a topographically complex landscape in a cold temperate mountain forest, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-13883, https://doi.org/10.5194/egusphere-egu25-13883, 2025.
Methane (CH4) is one the most important greenhouse gas and is responsible for approximatively 20% of the global warming (IPCC, 2022). Soils and mainly upland forest soils where aerobic environment prevails, are one of the main global sink of methane (Dutaur et Verchot 2013). At the soil-atmosphere interface, the net methane efflux consists in a net balance between the production of CH4 by methanogenic bacteria mainly in deep anaerobic soil layers and the consumption by methanotrophic bacteria in the aerobic soil horizons of the methane produced in the soil or diffusing from the atmosphere into the soil.
Presence of trees could influence soil edaphic features (mainly carbon content, pH, nitrogen, soil structure and texture, water content, …) which can have an impact on the abundance of methanotrophic and methanogenic communities in the soil profile and thus on methane uptake. In the upper part of the well aerated mineral soil, the abundance of methanotrophs is highest, but the depth of this level depends on the thickness of the organic layer and then on the rate of litter mineralisation. Depending on the season and the tree species in the plot, the intensity of methane uptake and the pattern of methane consumption may change.
The objective of this project was to study the influence of the temporal dynamics of methane consumption in a soil profile of different forest stand types. For this purpose, we developed a method to sample intact soil cores. We took 5 soil cores of 3 different thicknesses (5, 10 and 15 cm) in a forest of spruce, beech, oak and pine at different dates in spring 2022. Methane and CO2 fluxes were measured in the week after sampling on the soil cores incubated at 20°C.
Regardless of season, methane consumption increased with sample thickness. In the upper 5 cm, methane consumption was highest of the beech forest compared to the other stand types. However, when considering the 15 cm of soil, methane consumption no longer differed between stands. This trend seems to be related to the sharp decrease in organic carbon content and the much lower water content in spruce and pine forests. It is also possible that methane consumption at depth in the beech forest is limited by the low availability of methane at depth, which has been consumed at the top of the profile.
How to cite: Plain, C., Bras, N., and Epron, D.: Influence of sampling depth and stand species on the potential methane uptake of forest soil samples., EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-20015, https://doi.org/10.5194/egusphere-egu25-20015, 2025.
Forest fires are arguably one of the most destructive natural disturbances in the boreal forest biome and can cause significant changes to the carbon balance in these ecosystems. Although the area of forests burned annually in Fennoscandia is currently small (<1000 ha), this area may increase both due to biodiversity directives to increase habitat diversity using prescribed burning and due to climate change intensifying wildfire regimes. Fire severity impacts the biological, chemical, and physical properties of soils which underlie greenhouse gas (GHG) fluxes, which can interact to cause complex dynamics in GHG emissions for decades after fire. Therefore, it is essential to understand the impact of fire on forest soil GHG fluxes. Currently, upland forest soils in the boreal biome act as a weak methane (CH4) sink, but there are conflicting estimates about how these fluxes are impacted by forest fire. To better understand these dynamics and what the future may hold, we must quantify CH4 fluxes after fire and identify the factors that impact this, namely soil, vegetation, and fire characteristics.
We aimed to measure CH4 fluxes following prescribed restoration burning. Our research sites were thinned dry Scots pine (Pinus sylvestris) forest with sandy soils and sparse understorey vegetation at four locations in central Finland. We established permanent sample plots in each research site and installed collars for static chamber measurements. Plots were located in unburned, low-severity burn, and high-severity burn areas. Prescribed burning was conducted under suitable weather conditions, usually in the first half of June. Burning resulted in ground vegetation and logging debris were consumed across the site, but standing tree mortality varied between 0 and 100%. To measure CH4 fluxes from the soils, we used a dark static chamber and a portable trace gas analyzer (Licor LI-7810). CH4 fluxes were measured daily immediately after fire, then bi-monthly up to two growing seasons after prescribed burning.
Results indicate that CH4 uptake increased following fire, but this was not equal on all sites and varied over time. In terms of burn severity, we found that plots with low-severity burning had greater increases in CH4 uptake. Immediately following fire (i.e. when some active smoldering still present), we found that CH4 fluxes were highly variable and included very high CH4 emissions. We found no significant differences in soil CH4 fluxes between control and treated plots prior to burning, despite different forest management histories in some cases. Increased CH4 uptake in low severity plots is likely also linked to low microbe mortality, potential increases in microbe diversity, and soil temperature (Köster et al. 2011). However, a more complete understanding of the mechanisms and conditions that drive increases in CH4 uptake in low-severity burns requires further research.
How to cite: Kokkonen, N., Rebiffé, M., and Köster, K.: Post-fire methane fluxes from boreal forest soils depend on burn severity, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-16159, https://doi.org/10.5194/egusphere-egu25-16159, 2025.
