Methane emissions from tree stems: a new frontier in the global carbon cycle

Distinct microbial communities drive methane cycling in below- and above-ground compartments of tropical cloud forests growing on peat

Cloud forests are unique yet understudied ecosystems regarding CH4 exchange despite their significance in carbon storage. We investigated CH4 fluxes in peat soil and tree stems of two tropical cloud forests on Réunion Island, one featuring Erica reunionensis and the second a mix of E. reunionensis and Alsophila glaucifolia. The study examined microbiomes across below-ground (soil) and above-ground (canopy soil, leaves, and stems) forest compartments. Metagenomics and qPCR analyses targeted key genes in methanogenesis and methanotrophy in soil and above-ground samples, alongside soil physicochemical measurements. CH4 fluxes from peat soil and tree stems were measured using gas chromatography and portable trace gas analyzers. Peat soil in both forests acted as a CH4 sink (- 23.8 ± 4.84 µg C m- 2 h- 1) and CO2 source (55.5 ± 5.51 µg C m- 2 h- 1), with higher CH4 uptake in sites dominated by endemic tree species E. reunionensis. In forest soils, a high abundance of n-DAMO 16 S rRNA gene (3.42 × 107 ± 7 × 106 copies/g dw) was associated with nitrate levels and higher rates of CH4 uptake and CO2 emissions. NC-10 bacteria (0.1-0.3%) were detected in only the Erica forest soil, verrucomicrobial methanotrophs (0.1-3.1%) only in the mixed forest soil, whereas alphaproteobacterial methanotrophs (0.1-3.3%) were present in all soils. Tree stems in both forests were weak sinks of CH4 (-0.94 ± 0.4 µg C m- 2 h- 1). The canopy soil hosted verrucomicrobial methanotrophs (0.1-0.3%). The leaves in both forests exhibited metabolic potential for CH4 production, e.g., exhibiting high mcrA copy numbers (3.5 × 105 ± 2.3 × 105 copies/g dw). However, no CH4-cycling functional genes were detected in the stem core samples. Tropical cloud forest peat soils showed high anaerobic methanotrophy via the n-DAMO process, while aerobic methanotrophs were abundant in canopy soils. Leaves hosted methanotrophs but predominantly methanogens. These results highlight the significant differences between canopy and soil microbiomes in the CH4 cycle, emphasizing the importance of above-ground microbiomes in forest CH4 gas budgets.

Springtime soil and tree stem greenhouse gas fluxes and the related soil microbiome pattern in a drained peatland forest

Spring can be a critical time of year for stem and soil methane (CH4), nitrous oxide (N2O) and carbon dioxide (CO2) emissions as soil freeze-thaw events can be hot moments of gas release. Greenhouse gas fluxes from soil, Downy birch (Betula pubescens) and Norway spruce (Picea abies) stems were quantified using chamber systems and gas analysers in spring 2023 in a northern drained peatland forest. Dissolved gas concentrations in birch sap and soil water, environmental parameters, soil chemistry, and functional gene abundances in the soil were determined. During spring, initially low soil and stem CH4, N2O, and CO2 emissions increased towards late April. Temperature emerged as the primary driver of soil and stem fluxes, alongside photosynthetically active radiation influencing stem fluxes. Soil hydrologic conditions had minimal short-term impact. No clear evidence linked stem CH4 emissions to birch sap gas concentrations, while relationships existed for CO2. Functional gene abundances of the N and CH4-cycles changed between measurement days. Potential for methanogenesis and complete denitrification was higher under elevated soil water content, shifting to methanotrophy and incomplete denitrification as the study progressed. However, our results highlight the need for further analysis of relationships between microbial cycles and GHG fluxes under different environmental conditions, including identifying soil microbial processes in soil layers where tree roots absorb water.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10533-025-01238-3.

Insights into the subdaily variations in methane, nitrous oxide and carbon dioxide fluxes from upland tropical tree stems

Recent studies have shown that stem fluxes, although highly variable among trees, can alter the strength of the methane (CH4) sink or nitrous oxide (N2O) source in some forests, but the patterns and magnitudes of these fluxes remain unclear. This study investigated the drivers of subdaily and seasonal variations in stem and soil CH4, N2O and carbon dioxide (CO2) fluxes. CH4, N2O and CO2 fluxes were measured continuously for 19 months in individual stems of two tree species, Eperua falcata (Aubl.) and Lecythis poiteaui (O. Berg), and surrounding soils using an automated chamber system in an upland tropical forest. Subdaily variations in these fluxes were related to environmental and stem physiological (sap flow and stem diameter variations) measurements under contrasting soil water conditions. The results showed that physiological and climatic drivers only partially explained the subdaily flux variations. Stem CH4 and CO2 emissions and N2O uptake varied with soil water content, time of day and between individuals. Stem fluxes decoupled from soil fluxes. Our study contributes to understanding the regulation of stem greenhouse gas fluxes. It suggests that additional variables (e.g. internal gas concentrations, wood-colonising microorganisms, wood density and anatomy) may account for the remaining unexplained variability in stem fluxes, highlighting the need for further studies.

Global inland water greenhouse gas (GHG) geographical patterns and escape mechanisms under different water level

Inland water ecosystems are unique, whereby water level changes can lead to variance in greenhouse gas (GHG) emissions. The GHG circulation intensity of inland waterbodies is high, so different water depths affect the temperature sensitivity of greenhouse gases, and have different cooling effects on CO2 storage and warming effects on CH4 emissions, being a typical GHG conversion channel. This study systematically reveals geographical GHG emission patterns from inland waterbodies and GHG impact mechanisms from regional waterbodies. Special emphasis is also paid to compounded environmental impact changes on GHG emissions under water level regulations. Additionally, we explore how increases in primary productivity can convert aquatic ecosystems from CO2 sources to CO2 sinks. However, GHG formation and emissions under ecological reservoir water level fluctuations in flood-ebb zones, intertidal tidal zones, wetlands, and lacustrine systems remain uncertain compared with those under natural hydrological conditions. Therefore, mechanisms that control GHG exchange and production processes under water level changes must first be determined, especially regarding post flood hydrological-based drying effects on GHG flux at the water-air interface. Finally, we recommend instituting environmental management and water-level control measures to reduce GHG emissions, which are favorable for minimizing GHG flux while protecting ecosystem functions and biodiversity.

Tree stem-atmosphere greenhouse gas fluxes in a boreal riparian forest

Tree stems exchange greenhouse gases with the atmosphere but the magnitude, variability and drivers of these fluxes remain poorly understood. Here, we report stem fluxes of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) in a boreal riparian forest, and investigate their spatiotemporal variability and ecosystem level importance. For two years, we measured CO2 and CH4 fluxes on a monthly basis in 14 spruces (Picea abies) and 14 birches (Betula pendula) growing near a headwater stream affected by historic ditching. We also measured N2O fluxes on three occasions. All tree stems were net emitters of CO2 and CH4, while N2O fluxes were around zero. CO2 fluxes correlated strongly with air temperature and peaked in summer. CH4 fluxes correlated modestly with air temperature and solar radiation and peaked in late winter and summer. Trees with larger stem diameter emitted more CO2 and less CH4 and trees closer to the stream emitted more CO2 and CH4. The CO2 and CH4 fluxes did not differ between spruce and birch, but correlations of CO2 fluxes with stem diameter and distance to stream differed between the tree species. The absence of vertical trends in CO2 and CH4 fluxes along the stems and their low correlation with groundwater levels and soil CO2 and CH4 partial pressures suggest tree internal production as the primary source of stem emissions. At the ecosystem level, the stem CO2, CH4 and N2O emissions represented 52 ± 16 % of the forest floor CO2 emissions and 3 ± 1 % and 11 ± 40 % of the forest floor CH4 and N2O uptake, respectively, during the snow-free period (median ± SE). The six month snow-cover period contributed 11 ± 45 % and 40 ± 29 % to annual stem CO2 and CH4 emissions, respectively. Overall, the stem gas fluxes were more typical for upland rather than wetland ecosystems likely due to historic ditching and subsequent groundwater level decrease.

Foliar methane and nitrous oxide fluxes in tropical tree species

Methane (CH₄) and nitrous oxide (N₂O) are critical biogenic greenhouse gases (GHGs) with global warming potentials substantially greater than that of carbon dioxide (CO₂). The exchange of these gases in tropical forests, particularly via foliar processes, remains poorly understood. We quantified foliar CH₄ and N₂O fluxes among tropical tree species and examined their potential association with the leaf economics spectrum (LES) traits. Sampling within Lawachara National Park, Bangladesh, we used in-situ measurements of foliar CH₄ and N₂O fluxes employing off-axis integrated cavity output spectroscopy (CH₄, CO₂ and H₂O) and optical feedback-cavity enhanced absorption spectroscopy (N₂O) analyzers. Leaves were measured under dark, low, and high (0, 100, and 1000 μmol·m-2·s-1) light conditions. Surveyed tree species exhibited both net foliar uptake and efflux of CH₄, with a mean flux not different from zero, suggesting negligible net foliar emissions at the stand level. Plant families showed differences in CH₄, but not N₂O fluxes. Consistent efflux was observed for N₂O, with a mean of 0.562 ± 0.060 pmol·m-2·s-1. Pioneer species exhibited a higher mean N₂O flux (0.81 ± 0.17 pmol·m-2·s-1) compared to late-successional species (0.37 ± 0.05 pmol·m-2·s-1). Pioneer species also showed a trend toward a higher mean CH₄ flux (0.24 ± 0.21 nmol·m-2·s-1) compared to mid-successional (-0.01 ± 0.26 nmol·m-2·s-1) and late-successional species (-0.05 ± 0.28 nmol·m-2·s-1). Moreover, among all leaf traits within the leaf economic spectrum, a significant positive relationship was observed between leaf N₂O flux and total leaf nitrogen. Our results suggest that pioneer tree species significantly contribute to net CH₄ and N₂O emissions, potentially counteracting the carbon sequestration benefits in regenerating tropical forests. These findings indicate that accurate GHG budgeting should include direct measurements of foliar CH₄ and N₂O fluxes. Moreover, the results suggest that forest conservation and management strategies that prioritize late successional species will better mitigate GHG emissions.

Methane cycling in temperate forests

Temperate forest soils are considered significant methane (CH4) sinks, but other methane sources and sinks within these forests, such as trees, litter, deadwood, and the production of volatile organic compounds are not well understood. Improved understanding of all CH4 fluxes in temperate forests could help mitigate CH4 emissions from other sources and improve the accuracy of global greenhouse gas budgets. This review highlights the characteristics of temperate forests that influence CH4 flux and assesses the current understanding of the CH4 cycle in temperate forests, with a focus on those managed for specific purposes. Methane fluxes from trees, litter, deadwood, and soil, as well as the interaction of canopy-released volatile organic compounds on atmospheric methane chemistry are quantified, the processes involved and factors (biological, climatic, management) affecting the magnitude and variance of these fluxes are discussed. Temperate forests are unique in that they are extremely variable due to strong seasonality and significant human intervention. These features control CH4 flux and need to be considered in CH4 budgets. The literature confirmed that temperate planted forest soils are a significant CH4 sink, but tree stems are a small CH4 source. CH4 fluxes from foliage and deadwood vary, and litter fluxes are negligible. The production of volatile organic compounds could increase CH4's lifetime in the atmosphere, but current in-forest measurements are insufficient to determine the magnitude of any effect. For all sources and sinks more research is required into the mechanisms and microbial community driving CH4 fluxes. The variability in CH4 fluxes within each component of the forest, is also not well understood and has led to overestimation of CH4 fluxes when scaling up measurements to a forest or global scale. A roadmap for sampling and scaling is required to ensure that all CH4 sinks and sources within temperate forests are accurately accounted for and able to be included in CH4 budgets and models to ensure accurate estimates of the contribution of temperate planted forests to the global CH4 cycle.

Methane concentration in the heartwood of living trees in a cold temperate mountain forest: variation, transport and emission

Forest soils are the largest terrestrial sink of methane (CH4), but CH4 produced in tree trunks by methanogenic archaea and emitted into the atmosphere can significantly offset CH4 oxidation in the soil. However, our mechanistic understanding of CH4 accumulation in tree trunks, in relation to CH4 emission from the trunk surface, is still limited. We characterized temporal variations in the molar fraction of CH4 in the heartwood of trees ([CH4]HW) of four different species in a mountain forest and addressed the relationship between [CH4]HW and emission from the surface of the trunk (${F}_{CH_4}$), in connection with the characteristics of the wood. [CH4]HW measurements were made monthly for 15 months using gas-porous tubes permanently inserted into the trunk. [CH4]HW were above ambient CH4 molar fraction for all trees, lower than 100 p.p.m. for seven trees, higher for the nine other trees and greater than 200,000 p.p.m. (>20%) for two of these nine trees. [CH4]HW varied monthly but were not primarily determined by trunk temperature. Heartwood diffusive resistance for CH4 was variable between trees, not only due to heartwood characteristics but probably also related to source location. ${F}_{CH_4}$were weakly correlated with [CH4]HW measured a few days after. The resulting apparent diffusion coefficient was also variable between trees suggesting variations in the size and location of the CH4 production sites as well as resistance to gas transport within the trunk. Our results highlight the challenges that must be overcome before CH4 emissions can be simulated at the tree level.

Ubiquity of methanogenic archaea in the trunk of coniferous and broadleaved tree species in a mountain forest

Wetwood of living trees is a habitat of methanogenic archaea, but the ubiquity of methanogenic archaea in the trunk of various trees has not been revealed. The present study analysed methanogenic archaeal communities inside coniferous and broadleaved trees in a cold temperate mountain forest by culture-dependent or independent techniques. Heartwood and sapwood segments were obtained from the trunk of seven tree species, Cryptomeria japonica, Quercus crispula, Fraxinus mandshurica, Acer pictum, Aesculus turbinata, Magnolia obovata, and Populus tremula. Amplicon sequencing analysis of 16S rRNA genes showed that Methanobacteriaceae predominated the archaeal communities and Methanomassiliicoccaceae also inhabited some trees. Real-time PCR analysis detected methanogenic archaeal mcrA genes from all the tree species, with a maximum of 107 copies g-1 dry wood. Digital PCR analysis also detected mcrA genes derived from Methanobacterium spp. and Methanobrevibacter spp. from several samples, with a maximum of 105 and 104 copies g-1 dry wood. The enumeration by the most probable number method demonstrated the inhabitation of viable methanogenic archaea inside the trees; 106 cells g-1 dry wood was enumerated from a heartwood sample of C. japonica. Methanogenic archaea related to Methanobacterium beijingense were cultivated from a heartwood sample of Q. crispula and F. mandshurica. The present study demonstrated that the inside of various trees is a common habitat for methanogenic archaeal communities and a potential source of methane in forest ecosystems.

Methane sink of subterranean space in an integrated atmosphere-soil-cave system

CH4 serves as an important greenhouse gas, yet limited knowledge is available in global and regional CH4 cycling, particularly in widely distributed karst terrain. In this study, we investigated an upland in Puding Karst Ecosystem Research Station, and explored CH4 concentration and/or flux in atmosphere, soil and cave using a closed static chamber method and an eddy covariance system. Meanwhile, we monitored atmospheric temperature, precipitation, temperature and wind velocity in the cave entrance. The results demonstrated that atmospheric CH4 and actual soil CH4 fluxes in the source area of eddy covariance system were -0.19 ± 8.64 nmols-1m-2 and -0.16 nmols-1m-2 respectively. The CH4 concentrations in Shawan Cave exhibited 10 ∼ 100-fold lower than that of the external atmosphere. CH4 oxidation rate dominated by methane-oxidizing bacteria was 1.98 nmols-1m-2 in Shawan Cave when it combined with temperature difference between cave and external atmosphere. Therefore, CH4 sink in global karst subterranean spaces was estimated at 106.2 Tg CH4 yr-1. We supplemented an understanding of CH4 cycling paths and fluxes in karst terrain, as well as CH4 sinks in karst subterranean space. Further works require to establish a karst ecosystem observation network to conduct long-term integrated studies on CH4 fluxes regarding atmosphere, soils, plants and caves.

Microbial Communities in Standing Dead Trees in Ghost Forests are Largely Aerobic, Saprophytic, and Methanotrophic

Standing dead trees (snags) are recognized for their influence on methane (CH4) cycling in coastal wetlands, yet the biogeochemical processes that control the magnitude and direction of fluxes across the snag-atmosphere interface are not fully elucidated. Herein, we analyzed microbial communities and fluxes at one height from ten snags in a ghost forest wetland. Snag-atmosphere CH4 fluxes were highly variable (- 0.11-0.51 mg CH4 m-2 h-1). CH4 production was measured in three out of ten snags; whereas, CH4 consumption was measured in two out of ten snags. Potential CH4 production and oxidation in one core from each snag was assayed in vitro. A single core produced CH4 under anoxic and oxic conditions, at measured rates of 0.7 and 0.6 ng CH4 g-1 h-1, respectively. Four cores oxidized CH4 under oxic conditions, with an average rate of - 1.13 ± 0.31 ng CH4 g-1 h-1. Illumina sequencing of the V3/V4 region of the 16S rRNA gene sequence revealed diverse microbial communities and indicated oxidative decomposition of deadwood. Methanogens were present in 20% of the snags, with a mean relative abundance of < 0.0001%. Methanotrophs were identified in all snags, with a mean relative abundance of 2% and represented the sole CH4-cycling communities in 80% of the snags. These data indicate potential for microbial attenuation of CH4 emissions across the snag-atmosphere interface in ghost forests. A better understanding of the environmental drivers of snag-associated microbial communities is necessary to forecast the response of CH4 cycling in coastal ghost forest wetlands to a shifting coastal landscape.

Dry and wet periods determine stem and soil greenhouse gas fluxes in a northern drained peatland forest

Greenhouse gas (GHG) fluxes from peatland soils are relatively well studied, whereas tree stem fluxes have received far less attention. Simultaneous year-long measurements of soil and tree stem GHG fluxes in northern peatland forests are scarce, as previous studies have primarily focused on the growing season. We determined the seasonal dynamics of tree stem and soil CH4, N2O and CO2 fluxes in a hemiboreal drained peatland forest. Gas samples for flux calculations were manually collected from chambers at different heights on Downy Birch (Betula pubescens) and Norway Spruce (Picea abies) trees (November 2020-December 2021) and analysed using gas chromatography. Environmental parameters were measured simultaneously with fluxes and xylem sap flow was recorded during the growing season. Birch stems played a greater role in the annual GHG dynamics than spruce stems. Birch stems were net annual CH4, N2O and CO2 sources, while spruce stems constituted a CH4 and CO2 source but a N2O sink. Soil was a net CO2 and N2O source, but a sink of CH4. Temporal dynamics of stem CH4 and N2O fluxes were driven by isolated emissions' peaks that contributed significantly to net annual fluxes. Stem CO2 efflux followed a seasonal trend coinciding with tree growth phenology. Stem CH4 dynamics were significantly affected by the changes between wetter and drier periods, while N2O was more influenced by short-term changes in soil hydrologic conditions. We showed that CH4 emitted from tree stems during the wetter period can offset nearly half of the soil sink capacity. We presented for the first time the relationship between tree stem GHG fluxes and sap flow in a peatland forest. The net CH4 flux was likely an aggregate of soil-derived and stem-produced CH4. A dominating soil source was more evident for stem N2O fluxes.

Aerobic methane production in Scots pine shoots is independent of drought or photosynthesis

Shoot-level emissions of aerobically produced methane (CH4) may be an overlooked source of tree-derived CH4, but insufficient understanding of the interactions between their environmental and physiological drivers still prevents the reliable upscaling of canopy CH4 fluxes. We utilised a novel automated chamber system to continuously measure CH4 fluxes from the shoots of Pinus sylvestris (Scots pine) saplings under drought to investigate how canopy CH4 fluxes respond to the drought-induced alterations in their physiological processes and to isolate the shoot-level production of CH4 from soil-derived transport and photosynthesis. We found that aerobic CH4 emissions are not affected by the drought-induced stress, changes in physiological processes, or decrease in photosynthesis. Instead, these emissions vary on short temporal scales with environmental drivers such as temperature, suggesting that they result from abiotic degradation of plant compounds. Our study shows that aerobic CH4 emissions from foliage are distinct from photosynthesis-related processes. Thus, instead of photosynthesis rates, it is more reliable to construct regional and global estimates for the aerobic CH4 emission based on regional differences in foliage biomass and climate, also accounting for short-term variations of weather variables such as air temperature and solar radiation.

The challenge of estimating global termite methane emissions

Methane is a powerful greenhouse gas, more potent than carbon dioxide, and emitted from a variety of natural sources including wetlands, permafrost, mammalian guts and termites. As increases in global temperatures continue to break records, quantifying the magnitudes of key methane sources has never been more pertinent. Over the last 40 years, the contribution of termites to the global methane budget has been subject to much debate. The most recent estimates of termite emissions range between 9 and 15 Tg CH4 year-1, approximately 4% of emissions from natural sources (excluding wetlands). However, we argue that the current approach for estimating termite contributions to the global methane budget is flawed. Key parameters, namely termite methane emissions from soil, deadwood, living tree stems, epigeal mounds and arboreal nests, are largely ignored in global estimates. This omission occurs because data are lacking and research objectives, crucially, neglect variation in termite ecology. Furthermore, inconsistencies in data collection methods prohibit the pooling of data required to compute global estimates. Here, we summarise the advances made over the last 40 years and illustrate how different aspects of termite ecology can influence the termite contribution to global methane emissions. Additionally, we highlight technological advances that may help researchers investigate termite methane emissions on a larger scale. Finally, we consider dynamic feedback mechanisms of climate warming and land-use change on termite methane emissions. We conclude that ultimately the global contribution of termites to atmospheric methane remains unknown and thus present an alternative framework for estimating their emissions. To significantly improve estimates, we outline outstanding questions to guide future research efforts.

Rapid bark-mediated tree stem methane transport occurs independently of the transpiration stream in Melaleuca quinquenervia

Tree stem methane emissions are important components of lowland forest methane budgets. The potential for species-specific behaviour among co-occurring lowland trees with contrasting bark characteristics has not been investigated. We compare bark-mediated methane transport in two common lowland species of contrasting bark characteristics (Melaleuca quinquenervia featuring spongy/layered bark with longitudinally continuous airspaces and Casuarina glauca featuring hard/dense common bark) through several manipulative experiments. First, the progressive cutting through M. quinquenervia bark layers caused exponential increases in methane fluxes (c. 3 orders of magnitude); however, sapwood-only fluxes were lower, suggesting that upward/axial methane transport occurs between bark layers. Second, concentrated methane pulse-injections into exposed M. quinquenervia bark, revealed rapid axial methane transport rates (1.42 mm s-1 ), which were further supported through laboratory-simulated experiments (1.41 mm s-1 ). Laboratory-simulated radial CH4 diffusion rates (through bark) were c. 20-times slower. Finally, girdling M. quinquenervia stems caused a near-instantaneous decrease in methane flux immediately above the cut. By contrast, girdling C. glauca displayed persistent, though diminished, methane fluxes. Overall, the experiments revealed evidence for rapid 'between-bark' methane transport independent from the transpiration stream in M. quinquenervia, which facilitates diffusive axial transport from the rhizosphere and/or sapwood sources. This contrasts with the slower, radial 'through-bark' diffusive-dominated gas transportation in C. glauca.

Methane and nitrous oxide emissions and related microbial communities from mangrove stems on Qi'ao Island, Pearl River Estuary in China

Mangrove forests, crucial carbon-rich ecosystems, are increasingly vulnerable to soil carbon loss and greenhouse gas (GHG) emissions due to human disturbance. However, the contribution of mangrove trees to GHG emissions remains poorly understood. This study monitored CO2, CH4, and N2O fluxes from the stems of two mangrove species, native Kandelia obovata (KO) and exotic Sonneratia apetala (SA), at three heights (0.7 m, 1.2 m, and 1.7 m) during the dry winter period on Qi'ao Island, Pearl River Estuary, China. Heartwood samples were analyzed to identify potential functional groups related to gas fluxes. Our study found that tree stems acted as both sinks and sources for N2O (ranging from -9.49 to 28.35 μg m-2 h-1 for KO and from -6.73 to 28.95 μg m-2 h-1 for SA) and CH4. SA exhibited significantly higher stem CH4 flux (from -26.67 to 97.33 μg m-2 h-1) compared to KO (from -44.13 to 88.0 μg m-2 h-1) (P < 0.05). When upscaled to the community level, both species were net emitters of CH4, contributing approximately 4.68 % (KO) and 0.51 % (SA) to total CH4 emissions. The decrease in stem CH4 flux with increasing height, indicates a soil source. Microbial analysis in the heartwood using the KEGG database indicated aceticlastic methanogenesis as the dominant CH4 pathway. The presence of methanogens, methanotrophs, denitrifiers, and nitrifiers suggests microbial involvement in CH4 and N2O production and consumption. Remarkably, the dominance of Cyanobacteria in the heartwood microbiome (with the relative abundance of 97.5 ± 0.6 % for KO and 99.1 ± 0.2 % for SA) implies roles in carbon and nitrogen fixation for mangroves coping with nitrogen limitation in coastal wetlands, and possibly in CH4 production. Although the present study has limitations in sampling duration and area, it highlights the significant role of tree stems in GHG emissions which is crucial for a holistic evaluation of the global carbon sequestration capability of mangrove ecosystems. Future research should broaden spatial and temporal scales to enhance the accuracy of upscaling tree stem gas fluxes to the mangrove ecosystem level.

Plant-mediated CH4 exchange in wetlands: A review of mechanisms and measurement methods with implications for modelling

Plant-mediated CH4 transport (PMT) is the dominant pathway through which soil-produced CH4 can escape into the atmosphere and thus plays an important role in controlling ecosystem CH4 emission. PMT is affected by abiotic and biotic factors simultaneously, and the effects of biotic factors, such as the dominant plant species and their traits, can override the effects of abiotic factors. Increasing evidence shows that plant-mediated CH4 fluxes include not only PMT, but also within-plant CH4 production and oxidation due to the detection of methanogens and methanotrophs attached to the shoots. Despite the inter-species and seasonal differences, and the probable contribution of within-plant microbes to total plant-mediated CH4 exchange (PME), current process-based ecosystem models only estimate PMT based on the bulk biomass or leaf area index of aerenchymatous plants. We highlight five knowledge gaps to which more research efforts should be devoted. First, large between-species variation, even within the same family, complicates general estimation of PMT, and calls for further work on the key dominant species in different types of wetlands. Second, the interface (rhizosphere-root, root-shoot, or leaf-atmosphere) and plant traits controlling PMT remain poorly documented, but would be required for generalizations from species to relevant functional groups. Third, the main environmental controls of PMT across species remain uncertain. Fourth, the role of within-plant CH4 production and oxidation is poorly quantified. Fifth, the simplistic description of PMT in current process models results in uncertainty and potentially high errors in predictions of the ecosystem CH4 flux. Our review suggest that flux measurements should be conducted over multiple growing seasons and be paired with trait assessment and microbial analysis, and that trait-based models should be developed. Only then we are capable to accurately estimate plant-mediated CH4 emissions, and eventually ecosystem total CH4 emissions at both regional and global scales.

The hidden roots of wetland methane emissions

Wetlands are the largest natural source of methane (CH4 ) globally. Climate and land use change are expected to alter CH4 emissions but current and future wetland CH4 budgets remain uncertain. One important predictor of wetland CH4 flux, plants, play an important role in providing substrates for CH4 -producing microbes, increasing CH4 consumption by oxygenating the rhizosphere, and transporting CH4 from soils to the atmosphere. Yet, there remain various mechanistic knowledge gaps regarding the extent to which plant root systems and their traits influence wetland CH4 emissions. Here, we present a novel conceptual framework of the relationships between a range of root traits and CH4 processes in wetlands. Based on a literature review, we propose four main CH4 -relevant categories of root function: gas transport, carbon substrate provision, physicochemical influences and root system architecture. Within these categories, we discuss how individual root traits influence CH4 production, consumption, and transport (PCT). Our findings reveal knowledge gaps concerning trait functions in physicochemical influences, and the role of mycorrhizae and temporal root dynamics in PCT. We also identify priority research needs such as integrating trait measurements from different root function categories, measuring root-CH4 linkages along environmental gradients, and following standardized root ecology protocols and vocabularies. Thus, our conceptual framework identifies relevant belowground plant traits that will help improve wetland CH4 predictions and reduce uncertainties in current and future wetland CH4 budgets.

Methane emissions from tree stems - current knowledge and challenges: an introduction to a Virtual Issue

This article is a Commentary on the Virtual Issue ‘Methane emissions from tree stems – current knowledge and challenges’ that includes the following papers: Barba et al. (2019), Bréchet et al. (2021), Covey & Megonigal (2019), Feng et al. (2022), Flanagan et al. (2021), Jeffrey et al. (2019, 2021, 2023), Kohl et al. (2019), Machacova et al. (2021a,b, 2023), Megonigal et al. (2020), Pangala et al. (2013, 2014), Pitz & Megonigal (2017), Plain et al. (2019), Putkinen et al. (2021), Sjögersten et al. (2020), Takahashi et al. (2022), Tenhovirta et al. (2022), Wang et al. (2016), and Yip et al. (2018). Access the Virtual Issue at www.newphytologist.com/virtualissues.

A comprehensive review on methane's dual role: effects in climate change and potential as a carbon-neutral energy source

The unprecedented population and anthropogenic activity rise have challenged the future look up for shifts in global temperature and climate patterns. Anthropogenic activities such as land fillings, building dams, wetlands converting to lands, combustion of biomass, deforestation, mining, and the gas and coal industries have directly or indirectly increased catastrophic methane (CH4) emissions at an alarming rate. Methane is 25 times more potent trapping heat when compared to carbon dioxide (CO2) in the atmosphere. A rise in atmospheric methane, on a 20-year time scale, has an impact of 80 times greater than that of CO2. With increased population growth, waste generation is rising and is predicted to reach 6 Mt by 2025. CH4 emitted from landfills is a significant source that accounts for 40% of overall global methane emissions. Various mitigation and emissions reduction strategies could significantly reduce the global CH4 burden at a cost comparable to the parallel and necessary CO2 reduction measures, reversing the CH4 burden to pathways that achieve the goals of the Paris Agreement. CH4 mitigation directly benefits climate change, has collateral impacts on the economy, human health, and agriculture, and considerably supports CO2 mitigation. Utilizing the CO2 from the environment, methanogens produce methane and lower their carbon footprint. NGOs and the general public should act on time to overcome atmospheric methane emissions by utilizing the raw source for producing carbon-neutral fuel. However, more research potential is required for green energy production and to consider investigating the untapped potential of methanogens for dependable energy generation.

Model of methane transport in tree stems: Case study of sap flow and radial diffusion

The transport processes of methane (CH4 ) in tree stems remain largely unknown, although they are critical in assessing the whole-forest CH4 dynamics. We used a physically based dynamic model to study the spatial and diurnal dynamics of stem CH4 transport and fluxes. We parameterised the model using data from laboratory experiments with Pinus sylvestris and Betula pendula and compared the model to experimental data from a field study. Stem CH4 flux in laboratory and field conditions were explained by the axial advective CH4 transport from soil with xylem sap flow and the radial CH4 diffusion through the stem conditions. Diffusion resistance caused by the bark permeability did not significantly affect gas transport or stem CH4 flux in the laboratory experiments. The role of axial diffusion of CH4 in trees was unresolved and requires further studies. Due to the transit time of CH4 in the stem, the diurnal dynamics of stem CH4 fluxes can deviate markedly from the diurnal dynamics of sap flow.

Radiation and temperature drive diurnal variation of aerobic methane emissions from Scots pine canopy

Methane emissions from plant foliage may play an important role in the global methane cycle, but their size and the underlying source processes remain poorly understood. Here, we quantify methane fluxes from the shoots of Scots pine trees, a dominant tree species in boreal forests, to identify source processes and environmental drivers, and we evaluate whether these fluxes can be constrained at the ecosystem-level by eddy covariance flux measurements. We show that shoot-level measurements conducted in forest, garden, or greenhouse settings; on mature trees and saplings; manually and with an automated CO2-, temperature-, and water-controlled chamber system; and with multiple methane analyzers all resulted in comparable daytime fluxes (0.144 ± 0.019 to 0.375 ± 0.074 nmol CH4 g-1 foliar d.w. h-1). We further find that these emissions exhibit a pronounced diurnal cycle that closely follows photosynthetically active radiation and is further modulated by temperature. These diurnal patterns indicate that methane production is associated with diurnal cycle of sunlight, indicating that this production is either a byproduct of photosynthesis-associated biochemical reactions (e.g., the methionine cycle) or produced through nonenzymatic photochemical reactions in plant biomass. Moreover, we identified a light-dependent component in stand-level methane fluxes, which showed order-of-magnitude agreement with shoot-level measurements (0.968 ± 0.031 nmol CH4 g-1 h-1) and which provides an upper limit for shoot methane emissions.

Impacts of leaks and gas accumulation on closed chamber methods for measuring methane and carbon dioxide fluxes from tree stems

Accurate measurements of methane (CH4) and carbon dioxide (CO2) fluxes from tree stems are important for understanding greenhouse gas emissions. Closed chamber methods are commonly employed for this purpose; however, leaks between the chamber and the atmosphere as well as gas accumulation, known as the concentration buildup effect, can impact flux measurements significantly. In this study, we investigated the impacts of concentration buildup and leaks on semi-rigid closed chamber methods. Field measurements were conducted on six tree species, including three species from a Mexican mangrove ecosystem and three species from a Magellanic sub-Antarctic forest. Systematic observations revealed significant leak flow rates, ranging from 0.00 to 465 L h-1, with a median value of 1.25 ± 75.67 L h-1. We tested the efficacy of using cement to reduce leaks, achieving a leak flow rate reduction of 46-98 % without complete elimination. Our study also demonstrates a clear and substantial impact of concentration buildup on CH4 flux measurements, while CO2 flux measurements were relatively less affected across all tree species studied. Our results show that the combined effects of leaks and concentration buildup can lead to an underestimation of CH4 emissions by an average of 40 ± 20 % and CO2 emissions by 22 ± 22 %, depending on the bark roughness. Based on these findings, we recall a straightforward yet effective method to minimize experimental errors associated with these phenomena, previously established, and reiterated in the current context, for calculating emissions that considers effects of leaks and concentration buildup, while eliminating the need for separate determinations of these phenomena. Overall, the results, combined with a literature review, suggest that our current estimates of GHG flux from tree stems are currently underestimated.

Practical Guide to Measuring Wetland Carbon Pools and Fluxes

Wetlands cover a small portion of the world, but have disproportionate influence on global carbon (C) sequestration, carbon dioxide and methane emissions, and aquatic C fluxes. However, the underlying biogeochemical processes that affect wetland C pools and fluxes are complex and dynamic, making measurements of wetland C challenging. Over decades of research, many observational, experimental, and analytical approaches have been developed to understand and quantify pools and fluxes of wetland C. Sampling approaches range in their representation of wetland C from short to long timeframes and local to landscape spatial scales. This review summarizes common and cutting-edge methodological approaches for quantifying wetland C pools and fluxes. We first define each of the major C pools and fluxes and provide rationale for their importance to wetland C dynamics. For each approach, we clarify what component of wetland C is measured and its spatial and temporal representativeness and constraints. We describe practical considerations for each approach, such as where and when an approach is typically used, who can conduct the measurements (expertise, training requirements), and how approaches are conducted, including considerations on equipment complexity and costs. Finally, we review key covariates and ancillary measurements that enhance the interpretation of findings and facilitate model development. The protocols that we describe to measure soil, water, vegetation, and gases are also relevant for related disciplines such as ecology. Improved quality and consistency of data collection and reporting across studies will help reduce global uncertainties and develop management strategies to use wetlands as nature-based climate solutions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13157-023-01722-2.

Plant phenology and species-specific traits control plant CH4 emissions in a northern boreal fen

Aerenchymatic transport is an important mechanism through which plants affect methane (CH₄ ) emissions from peatlands. Controlling environmental factors and the effects of plant phenology remain, however, uncertain. We identified factors controlling seasonal CH₄ flux rate and investigated transport efficiency (flux rate per unit of rhizospheric porewater CH₄ concentration). We measured CH₄ fluxes through individual shoots of Carex rostrata, Menyanthes trifoliata, Betula nana and Salix lapponum throughout growing seasons in 2020 and 2021 and Equisetum fluviatile and Comarum palustre in high summer 2021 along with water-table level, peat temperature and porewater CH₄ concentration. CH₄ flux rate of C. rostrata was related to plant phenology and peat temperature. Flux rates of M. trifoliata and shrubs B. nana and S. lapponum were insensitive to the investigated environmental variables. In high summer, flux rate and efficiency were highest for C. rostrata (6.86 mg m^-2  h^-1 and 0.36 mg m^-2  h^-1 (μmol l^-1 )^-1 , respectively). Menyanthes trifoliata showed a high flux rate, but limited efficiency. Low flux rates and efficiency were detected for the remaining species. Knowledge of the species-specific CH₄ flux rate and their different responses to plant phenology and environmental factors can significantly improve the estimation of ecosystem-scale CH₄ dynamics in boreal peatlands.

Methane emission from stems of European beech (Fagus sylvatica) offsets as much as half of methane oxidation in soil

Trees are known to be atmospheric methane (CH₄ ) emitters. Little is known about seasonal dynamics of tree CH₄ fluxes and relationships to environmental conditions. That prevents the correct estimation of net annual tree and forest CH₄ exchange. We aimed to explore the contribution of stem emissions to forest CH₄ exchange. We determined seasonal CH₄ fluxes of mature European beech (Fagus sylvatica) stems and adjacent soil in a typical temperate beech forest of the White Carpathians with high spatial heterogeneity in soil moisture. The beech stems were net annual CH₄ sources, whereas the soil was a net CH₄ sink. High CH₄ emitters showed clear seasonality in their stem CH₄ emissions that followed stem CO₂ efflux. Elevated CH₄ fluxes were detected during the vegetation season. Observed high spatial variability in stem CH₄ emissions was neither explicably by soil CH₄ exchange nor by CH₄ concentrations, water content, or temperature studied in soil profiles near each measured tree. The stem CH₄ emissions offset the soil CH₄ uptake by up to 46.5% and on average by 13% on stand level. In Central Europe, widely grown beech contributes markedly to seasonal dynamics of ecosystem CH₄ exchange. Its contribution should be included into forest greenhouse gas flux inventories.

Evaluation of primers for the detection of deadwood-inhabiting archaea via amplicon sequencing

Archaea have been reported from deadwood of a few different tree species in temperate and boreal forest ecosystems in the past. However, while one of their functions is well linked to methane production any additional contribution to wood decomposition is not understood and underexplored which may be also attributed to lacking investigations on their diversity in this substrate. With this current work, we aim at encouraging further investigations by providing aid in primer choice for DNA metabarcoding using Illumina amplicon sequencing. We tested 16S primer pairs on genomic DNA extracted from woody tissue of four temperate deciduous tree species. Three primer pairs were specific to archaea and one prokaryotic primer pair theoretically amplifies both, bacterial and archaeal DNA. Methanobacteriales and Methanomassiliicoccales have been consistently identified as dominant orders across all datasets but significant variability in ASV richness was observed using different primer combinations. Nitrososphaerales have only been identified when using archaea-specific primer sets. In addition, the most commonly applied primer combination targeting prokaryotes in general yielded the lowest relative proportion of archaeal sequences per sample, which underlines the fact, that using target specific primers unraveled a yet unknown diversity of archaea in deadwood. Hence, archaea seem to be an important group of the deadwood-inhabiting community and further research is needed to explore their role during the decomposition process.

Spatiotemporal patterns and drivers of stem methane flux from two poplar forests with different soil textures

In forest ecosystems, the majority of methane (CH4) research focuses on soils, whereas tree stem CH4 flux and driving factors remain poorly understood. We measured the in situ stem CH4 flux using the static chamber-gas chromatography method at different heights in two poplar (Populus spp.) forests with separate soil textures. We evaluated the relationship between stem CH4 fluxes and environmental factors with linear mixed models and estimated the tree CH4 emission rate at the stand level. Our results showed that poplar stems were a net source of atmospheric CH4. The mean stem CH4 emission rates were 97.51 ± 6.21 μg·m-2·h-1 in Sihong and 67.04 ± 5.64 μg·m-2·h-1 in Dongtai. The stem CH4 emission rate in Sihong with clay loam soils was significantly higher (P < 0.001) than that in Dongtai with sandy loam soils. The stem CH4 emission rate also showed a seasonal variation, minimum in winter and maximum in summer. The stem CH4 emission rate generally decreased with increasing sampling height. Although the differences in CH4 emission rates between stem heights were significant in the annual averages, these differences were driven by differences observed in the summer. Stem CH4 emission rates were significantly and positively correlated with air temperature (P < 0.001), relative humidity (P < 0.001), soil water content (P < 0.001) and soil CH4 flux (P < 0.001). At these sites, the soil emitted CH4 to the atmosphere in summer (mainly from June to September) but absorbed CH4 from the atmosphere during the other season. At the stand level, tree CH4 emissions accounted for 2-35.4% of soil CH4 uptake. Overall, tree stem CH4 efflux could be an important component of the forest CH4 budget. Therefore, it is necessary to conduct more in situ monitoring of stem CH4 flux to accurately estimate the CH4 budget in the future.

Methane emissions from trees planted on a closed landfill site

Trees have morphological adaptations that allow methane (CH₄) generated below ground to bypass oxidation in aerobic surface soils. This natural phenomenon however has not been measured in a landfill context where planted trees may alter the composition and magnitude of CH₄ fluxes from the surface. To address this research gap, we measured tree stem and soil greenhouse gas (GHG) emissions (CH₄ and CO₂) from a closed UK landfill and comparable natural site, using an off-axis integrated cavity output spectroscopy analyser and flux chambers. Analyses showed average CH₄ stem fluxes from the landfill and non-landfill sites were 31.8 ± 24.4 µg m^-2 h^-1 and -0.3 ± 0.2 µg m^-2 h^-1, respectively. The landfill site showed seasonal patterns in CH₄ and CO₂ stem emissions, but no significant patterns were observed in CH₄ and CO₂ fluxes at different stem heights or between tree species. Tree stem emissions accounted for 39% of the total CH₄ surface flux (7% of the CO₂); a previously unknown contribution that should be included in future carbon assessments.

Insights into the mechanism of diurnal variations in methane emission from the stem surfaces of Alnus japonica

Recent studies have suggested that in certain environments, tree stems emit methane (CH₄ ). This study explored the mechanism of CH₄ emission from the stem surfaces of Alnus japonica in a riparian wetland. Stem CH₄ emission rates and sap flux were monitored year-round, and fine-root anatomy was investigated. CH₄ emission rates were estimated using a closed-chamber method. Sap flux was measured using Granier-type thermal dissipation probes. Root anatomy was studied using both optical and cryo-scanning electron microscopy. CH₄ emissions during the leafy season exhibited a diurnally changing component superimposed upon an underlying continuum in which the diurnal variation was in phase with sap flux. We propose a model in which stem CH₄ emission involves at least two processes: a sap flux-dependent component responsible for the diurnal changes, and a sap flux-independent component responsible for the background continuum. The contribution ratios of the two processes are season-dependent. The background continuum possibly resulted from the diffusive transport of gaseous CH₄ from the roots to the upper trunk. Root anatomy analysis indicated that the intercellular space of the cortex and empty xylem cells in fine roots could serve as a passageway for transport of gaseous CH₄ .

Solar radiation drives methane emissions from the shoots of Scots pine

Plants are recognized as sources of aerobically produced methane (CH₄ ), but the seasonality, environmental drivers and significance of CH₄ emissions from the canopies of evergreen boreal trees remain poorly understood. We measured the CH₄ fluxes from the shoots of Pinus sylvestris (Scots pine) and Picea abies (Norway spruce) saplings in a static, non-steady-state chamber setup to investigate if the shoots of boreal conifers are a source of CH₄ during spring. We found that the shoots of Scots pine emitted CH₄ and these emissions correlated with the photosynthetically active radiation. For Norway spruce, the evidence for CH₄ emissions from the shoots was inconclusive. Our study shows that the canopies of evergreen boreal trees are a potential source of CH₄ in the spring and that these emissions are driven by a temperature-by-light interaction effect of solar radiation either directly or indirectly through its effects on tree physiological processes.

Long-term dynamics of soil, tree stem and ecosystem methane fluxes in a riparian forest

The carbon (C) budgets of riparian forests are sensitive to climatic variability. Therefore, riparian forests are hot spots of C cycling in landscapes. Only a limited number of studies on continuous measurements of methane (CH₄) fluxes from riparian forests is available. Here, we report continuous high-frequency soil and ecosystem (eddy-covariance; EC) measurements of CH₄ fluxes with a quantum cascade laser absorption spectrometer for a 2.5-year period and measurements of CH₄ fluxes from tree stems using manual chambers for a 1.5 year period from a temperate riparian Alnus incana forest. The results demonstrate that the riparian forest is a minor net annual sink of CH₄ consuming 0.24 kg CH₄-C ha^-1 y^-1. Soil water content is the most important determinant of soil, stem, and EC fluxes, followed by soil temperature. There were significant differences in CH₄ fluxes between the wet and dry periods. During the wet period, 83% of CH₄ was emitted from the tree stems while the ecosystem-level emission was equal to the sum of soil and stem emissions. During the dry period, CH₄ was substantially consumed in the soil whereas stem emissions were very low. A significant difference between the EC fluxes and the sum of soil and stem fluxes during the dry period is most likely caused by emission from the canopy whereas at the ecosystem level the forest was a clear CH₄ sink. Our results together with past measurements of CH₄ fluxes in other riparian forests suggest that temperate riparian forests can be long-term CH₄ sinks.

Methane emissions may be driven by hydrogenotrophic methanogens inhabiting the stem tissues of poplar

Living trees in forests emit methane (CH₄ ) from their stems. However, the magnitudes, patterns, drivers, origins, and biogeochemical pathways of these emissions remain poorly understood. We measured in situ CH₄ fluxes in poplar stems and soils using static chambers and investigated the microbial communities of heartwood and sapwood by sequencing bacterial 16S, archaeal 16S, and fungal ITS rRNA genes. Methane emissions from poplar stems occurred throughout the sampling period. The mean CH₄ emission rate was 2.7 mg m^-2  stem d^-1 . Stem CH₄ emission rate increased significantly with air temperature, humidity, soil water content, and soil CH₄ fluxes, but decreased with increasing sampling height. The CO₂ reduction and methylotrophic methanogenesis were the major methanogenic pathways in wood tissues. The dominant methanogen groups detected in stem tissues were Methanobacterium, Methanobrevibacter, Rice Cluster I, Methanosarcina, Methanomassiliicoccus, Methanoculleus, and Methanomethylophilaceae. In addition, three methanotrophic genera were identified in the heartwood and sapwood - Methylocystis, Methylobacterium, and Paracoccus. Overall, stem CH₄ emissions can originate directly from the internal tissues or co-occur from soils and stems. The co-existence of methanogens and methanotrophs within heartwood and sapwood highlights a need for future research in the microbial mechanisms underlying stem CH₄ exchange with the atmosphere.

Spatiotemporal variability and origin of CO2 and CH4 tree stem fluxes in an upland forest

The exchange of multiple greenhouse gases (i.e., CO₂ and CH₄ ) between tree stems and the atmosphere represents a knowledge gap in the global carbon cycle. Stem CO₂ and CH₄ fluxes vary across time and space and are unclear, which are their individual or shared drivers. Here we measured CO₂ and CH₄ fluxes at different stem heights combining manual (biweekly; n = 678) and automated (hourly; n > 38,000) measurements in a temperate upland forest. All trees showed CO₂ and CH₄ emissions despite 20% of measurements showing net CH₄ uptake. Stem CO₂ fluxes presented clear seasonal trends from manual and automated measurements. Only automated measurements captured the high temporal variability of stem CH₄ fluxes revealing clear seasonal trends. Despite that temporal integration, the limited number of automated chambers made stand-level mean CH₄ fluxes sensitive to "hot spots," resulting in mean fluxes with high uncertainty. Manual measurements provided better integration of spatial variability, but their lack of temporal variability integration hindered the detection of temporal trends and stand-level mean fluxes. These results highlight the potential bias of previous studies of stem CH₄ fluxes solely based on manual or automated measurements. Stem height, temperature, and soil moisture only explained 7% and 11% of the stem CH₄ flux variability compared to 42% and 81% for CO₂ (manual and automated measurements, respectively). This large unexplained variability, in combination with high CH₄ concentrations in the trees' heartwood, suggests that stem CH₄ fluxes might be more influenced by gas transport and diffusivity through the wood than by drivers of respiratory CO₂ flux, which has crucial implications for developing process-based ecosystem models. We postulate that CH₄ is likely originated within tree stems because of lack of a consistent vertical pattern in CH₄ fluxes, evidence of CH₄ production in wood incubations, and low CH₄ concentration in the soil profile but high concentrations within the trees' heartwood.

Source or sink? A study on the methane flux from mangroves stems in Zhangjiang estuary, southeast coast of China

Mangrove ecosystems are an important component of "blue carbon". However, it is not clear whether the stems play roles in the CH₄ budget of mangrove ecosystems. This study investigated the CH₄ emission from mangrove stems and its potential driving factors. We set up six sample plots in the Zhangjiang Estuary National Mangrove Nature Reserve, where Kandelia obovata, Avicennia marina and Aegiceras corniculata are the main mangrove tree species. Soil properties such as total carbon content, redox potential and salinity were determined in each plot. The dynamic chamber method was used to measure mangrove stems and soil CH₄ fluxes. Combined field survey results with Principal Component Analysis (PCA) of soil properties, we divided the six plots into two sites (S1 and S2) to perform statistical analyses of stem CH₄ fluxes. Then the CH₄ fluxes from mangrove tree stems and soil were further scaled up to the ecosystem level through the mapping model. Under different backgrounds of soil properties, salinity and microbial biomass carbon were the main factors modified soil CH₄ fluxes in the two sites, and further affected the stem CH₄ fluxes of mangroves. The soil of both sites are sources of CH₄, and the soil CH₄ emission of S2 was about twice higher than that of S1. Results of upscaling model showed that mangrove stems in S1 were CH₄ sinks with -105.65 g d^-1. But stems in S2 were CH₄ sources around 1448.24 g d^-1. Taken together, our results suggested that CH₄ emission from mangrove soils closely depends on soils properties. And mangrove stems were found to act as both CH₄ sources and CH₄ sinks depend on soil CH₄ production. Therefore, when calculating the CH₄ budget of the mangrove ecosystem, the contribution of mangrove plant stems cannot be ignored.

New insight to the role of microbes in the methane exchange in trees: evidence from metagenomic sequencing

Methane (CH₄ ) exchange in tree stems and canopies and the processes involved are among the least understood components of the global CH₄ cycle. Recent studies have focused on quantifying tree stems as sources of CH₄ and understanding abiotic CH₄ emissions in plant canopies, with the role of microbial in situ CH₄ formation receiving less attention. Moreover, despite initial reports revealing CH₄ consumption, studies have not adequately evaluated the potential of microbial CH₄ oxidation within trees. In this paper, we discuss the current level of understanding on these processes. Further, we demonstrate the potential of novel metagenomic tools in revealing the involvement of microbes in the CH₄ exchange of plants, and particularly in boreal trees. We detected CH₄ -producing methanogens and novel monooxygenases, potentially involved in CH₄ consumption, in coniferous plants. In addition, our field flux measurements from Norway spruce (Picea abies) canopies demonstrate both net CH₄ emissions and uptake, giving further evidence that both production and consumption are relevant to the net CH₄ exchange. Our findings, together with the emerging diversity of novel CH₄ -producing microbial groups, strongly suggest microbial analyses should be integrated in the studies aiming to reveal the processes and drivers behind plant CH₄ exchange.

Diurnal Tree Stem CH4 and N2O Flux Dynamics from a Riparian Alder Forest

Tree stems play an important role in forest methane (CH4) and nitrous oxide (N2O) flux dynamics. Our paper aimed to determine the unknown diurnal variability of CH4 and N2O exchange in grey alder tree stems. The gas fluxes in tree stems and adjacent soil were measured using manual static and dynamic chamber systems with gas chromatographic and laser-spectroscopic analysis, respectively. The alder trees were predominant emitters of CH4 and N2O; however, N2O emission from stems was negligible. The soil mainly emitted N2O into the atmosphere and was both a source and sink of CH4, depending on environmental conditions. Neither the tree stems nor the riparian forest soil showed significant differences in their CH4 and N2O fluxes between the daytime and nighttime, independently of the exchange rates. In contrast to several previous studies revealing a diurnal variability of greenhouse gas fluxes from tree stems, our investigation did not show any clear daytime–nighttime differences. On the other hand, we found quite clear seasonal dynamics initiated by changing environmental conditions, such as temperature and soil water conditions and tree physiological activity. Our results imply a transport role of tree stems for soil-produced CH4 and N2O rather than the production of these gases in tree tissues, even though this cannot be excluded.

Isotopic evidence for axial tree stem methane oxidation within subtropical lowland forests

Knowledge regarding mechanisms moderating methane (CH₄ ) sink/source behaviour along the soil-tree stem-atmosphere continuum remains incomplete. Here, we applied stable isotope analysis (δ¹³ C-CH₄ ) to gain insights into axial CH₄ transport and oxidation in two globally distributed subtropical lowland species (Melaleuca quinquenervia and Casuarina glauca). We found consistent trends in CH₄ flux (decreasing with height) and δ¹³ C-CH₄ enrichment (increasing with height) in relation to stem height from ground. The average lower tree stem δ¹³ C-CH₄ (0-40 cm) of Melaleuca and Casuarina (-53.96‰ and -65.89‰) were similar to adjacent flooded soil CH₄ ebullition (-52.87‰ and -62.98‰), suggesting that stem CH₄ is derived mainly by soil sources. Upper stems (81-200 cm) displayed distinct δ¹³ C-CH₄ enrichment (Melaleuca -44.6‰ and Casuarina -46.5‰, respectively). Coupled 3D-photogrammetry with novel 3D-stem measurements revealed distinct hotspots of CH₄ flux and isotopic fractionation on Melaleuca, which were likely due to bark anomalies in which preferential pathways of gas efflux were enhanced. Diel experiments revealed greater δ¹³ C-CH₄ enrichment and higher oxidation rates in the afternoon, compared with the morning. Overall, we estimated that c. 33% of the methane was oxidised between lower and upper stems during axial transport, therefore potentially representing a globally significant, yet previously unaccounted for, methane sink.

Substantial hysteresis in emergent temperature sensitivity of global wetland CH4 emissions

Wetland methane (CH4) emissions ([Formula: see text]) are important in global carbon budgets and climate change assessments. Currently, [Formula: see text] projections rely on prescribed static temperature sensitivity that varies among biogeochemical models. Meta-analyses have proposed a consistent [Formula: see text] temperature dependence across spatial scales for use in models; however, site-level studies demonstrate that [Formula: see text] are often controlled by factors beyond temperature. Here, we evaluate the relationship between [Formula: see text] and temperature using observations from the FLUXNET-CH4 database. Measurements collected across the globe show substantial seasonal hysteresis between [Formula: see text] and temperature, suggesting larger [Formula: see text] sensitivity to temperature later in the frost-free season (about 77% of site-years). Results derived from a machine-learning model and several regression models highlight the importance of representing the large spatial and temporal variability within site-years and ecosystem types. Mechanistic advancements in biogeochemical model parameterization and detailed measurements in factors modulating CH4 production are thus needed to improve global CH4 budget assessments.

Bark-dwelling methanotrophic bacteria decrease methane emissions from trees

Tree stems are an important and unconstrained source of methane, yet it is uncertain whether internal microbial controls (i.e. methanotrophy) within tree bark may reduce methane emissions. Here we demonstrate that unique microbial communities dominated by methane-oxidising bacteria (MOB) dwell within bark of Melaleuca quinquenervia, a common, invasive and globally distributed lowland species. In laboratory incubations, methane-inoculated M. quinquenervia bark mediated methane consumption (up to 96.3 µmol m^-2 bark d^-1) and reveal distinct isotopic δ¹³C-CH₄ enrichment characteristic of MOB. Molecular analysis indicates unique microbial communities reside within the bark, with MOB primarily from the genus Methylomonas comprising up to 25 % of the total microbial community. Methanotroph abundance was linearly correlated to methane uptake rates (R² = 0.76, p = 0.006). Finally, field-based methane oxidation inhibition experiments demonstrate that bark-dwelling MOB reduce methane emissions by 36 ± 5 %. These multiple complementary lines of evidence indicate that bark-dwelling MOB represent a potentially significant methane sink, and an important frontier for further research.

Short-lived peaks of stem methane emissions from mature black alder (Alnus glutinosa (L.) Gaertn.) - Irrelevant for ecosystem methane budgets?

Tree stems can be a source of the greenhouse gas methane (CH4). However, assessments of the global importance of stem CH4 emissions are complicated by a lack of research and high variability between individual ecosystems. Here, we determined the contribution of emissions from stems of mature black alder (Alnus glutinosa (L.) Gaertn.) to overall CH4 exchange in two temperate peatlands. We measured emissions from stems and soils using closed chambers in a drained and an undrained alder forest over 2 years. Furthermore, we studied the importance of alder leaves as substrate for methanogenesis in an incubation experiment. Stem CH4 emissions were short-lived and occurred only during times of inundation at the undrained site. The drained site did not show stem emissions and the soil acted as a small CH4 sink. The contribution of stem emissions to the overall CH4 budget was below 0.3% in both sites. Our results show that mature black alder can be an intermittent source of CH4 to the atmosphere. However, the low share of stem CH4 emissions in both investigated stands indicates that this pathway may be of minor relative importance in temperate peatlands, yet strongly depend on the hydrologic regime.

Trees as net sinks for methane (CH4 ) and nitrous oxide (N2 O) in the lowland tropical rain forest on volcanic Réunion Island

Trees are known to emit methane (CH₄ ) and nitrous oxide (N₂ O), with tropical wetland trees being considerable CH₄ sources. Little is known about CH₄ and especially N₂ O exchange of trees growing in tropical rain forests under nonflooded conditions. We determined CH₄ and N₂ O exchange of stems of six dominant tree species, cryptogamic stem covers, soils and volcanic surfaces at the start of the rainy season in a 400-yr-old tropical lowland rain forest situated on a basaltic lava flow (Réunion Island). We aimed to understand the unknown role in greenhouse gas fluxes of these atypical tropical rain forests on basaltic lava flows. The stems studied were net sinks for atmospheric CH₄ and N₂ O, as were cryptogams, which seemed to be co-responsible for the stem uptake. In contrast with more commonly studied rain forests, the soil and previously unexplored volcanic surfaces consumed CH₄ . Their N₂ O fluxes were negligible. Greenhouse gas uptake potential by trees and cryptogams constitutes a novel and unique finding, thus showing that plants can serve not only as emitters, but also as consumers of CH₄ and N₂ O. The volcanic tropical lowland rain forest appears to be an important CH₄ sink, as well as a possible N₂ O sink.

Multiple processes contribute to methane emission in a riparian cottonwood forest ecosystem

Methane emission from trees may partially or completely offset the methane sink in upland soils, the only process that has been regularly included in methane budgets for forest ecosystems. Our objective was to analyze multiple biogeochemical processes that influence the production, oxidation and transport of methane in a riparian cottonwood ecosystem and its adjacent river. We combined chamber flux measurements on tree stems, forest soil and the river surface with eddy covariance measurements of methane net ecosystem exchange. In addition, we tested whether methanogens were present in cottonwood stems, shallow soil layers and alluvial groundwater. Average midday peak in net methane emission measured by eddy covariance was c. 12 nmol m^-2  s^-1 . The average uptake of methane by soils (0.87 nmol m^-2  s^-1 ) was largely offset by tree stem methane emission (0.75 nmol m^-2  s^-1 ). There was evidence of methanogens in tree stems but not in shallow soil. Growing season (May-September) cumulative net methane emission (17.4 mmol CH₄  m^-2 ) included methane produced in cottonwood stems and methane input to the nocturnal boundary layer from the forest and the adjacent river. The multiple processes contributing to methane emission illustrated the linked nature of these adjacent terrestrial and aquatic ecosystems.

Long-term effects of forest fires on soil greenhouse gas emissions and extracellular enzyme activities in a hemiboreal forest

Fire is the most important natural disturbance in boreal forests, and it has a major role regulating the carbon (C) budget of these systems. With the expected increase in fire frequency, the greenhouse gas (GHG) budget of boreal forest soils may change. In order to understand the long-term nature of the soil-atmosphere GHG exchange after fire, we established a fire chronosequence representing successional stages at 8, 19, 34, 65, 76 and 179 years following stand-replacing fires in hemiboreal Scots pine forests in Estonia. Changes in extracellular activity, litter decomposition, vegetation biomass, and soil physicochemical properties were assessed in relation to carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O) emissions. Soil temperature was highest 8 years after fire, whereas soil moisture varied through the fire chronosequences without a consistent pattern. Litter decomposition and CO₂ efflux were still lower 8 years after fire compared with pre-fire levels (179 years after fire). Both returned to pre-fire levels before vegetation re-established, and CO₂ efflux was only strongly responsive to temperature from 19 years after fire onward. Recovery of CO₂ efflux in the long term was associated with a moderate effect of fire on enzyme activity, the input of above- and below-ground litter carbon, and the re-establishment of vegetation. Soil acted as a CH₄ sink and N₂O source similarly in all successional stages. Compared with soil moisture and time after fire, soil temperature was the most important predictor for both GHGs. The re-establishment of overstorey and vegetation cover (mosses and lichens) might have caused an increase in CH₄ and N₂O effluxes in the studied areas, respectively.

Impact of forest plantation on methane emissions from tropical peatland

Tropical peatlands are a known source of methane (CH4 ) to the atmosphere, but their contribution to atmospheric CH4 is poorly constrained. Since the 1980s, extensive areas of the peatlands in Southeast Asia have experienced land-cover change to smallholder agriculture and forest plantations. This land-cover change generally involves lowering of groundwater level (GWL), as well as modification of vegetation type, both of which potentially influence CH4 emissions. We measured CH4 exchanges at the landscape scale using eddy covariance towers over two land-cover types in tropical peatland in Sumatra, Indonesia: (a) a natural forest and (b) an Acacia crassicarpa plantation. Annual CH4 exchanges over the natural forest (9.1 ± 0.9 g CH4  m-2  year-1 ) were around twice as high as those of the Acacia plantation (4.7 ± 1.5 g CH4  m-2  year-1 ). Results highlight that tropical peatlands are significant CH4 sources, and probably have a greater impact on global atmospheric CH4 concentrations than previously thought. Observations showed a clear diurnal variation in CH4 exchange over the natural forest where the GWL was higher than 40 cm below the ground surface. The diurnal variation in CH4 exchanges was strongly correlated with associated changes in the canopy conductance to water vapor, photosynthetic photon flux density, vapor pressure deficit, and air temperature. The absence of a comparable diurnal pattern in CH4 exchange over the Acacia plantation may be the result of the GWL being consistently below the root zone. Our results, which are among the first eddy covariance CH4 exchange data reported for any tropical peatland, should help to reduce the uncertainty in the estimation of CH4 emissions from a globally important ecosystem, provide a more complete estimate of the impact of land-cover change on tropical peat, and develop science-based peatland management practices that help to minimize greenhouse gas emissions.