Unraveling microbial processes involved in carbon and nitrogen cycling and greenhouse gas emissions in rewetted peatlands by molecular biology.

Restoration of drained peatlands through rewetting has recently emerged as a prevailing strategy to mitigate excessive greenhouse gas emissions and re-establish the vital carbon sequestration capacity of peatlands. Rewetting can help to restore vegetation communities and biodiversity, while still allowing for extensive agricultural management such as paludiculture. Belowground processes governing carbon fluxes and greenhouse gas dynamics are mediated by a complex network of microbial communities and processes. Our understanding of this complexity and its multi-factorial controls in rewetted peatlands is limited. Here, we summarize the research regarding the role of soil microbial communities and functions in driving carbon and nutrient cycling in rewetted peatlands including the use of molecular biology techniques in understanding biogeochemical processes linked to greenhouse gas fluxes. We emphasize that rapidly advancing molecular biology approaches, such as high-throughput sequencing, are powerful tools helping to elucidate the dynamics of key biogeochemical processes when combined with isotope tracing and greenhouse gas measuring techniques. Insights gained from the gathered studies can help inform efficient monitoring practices for rewetted peatlands and the development of climate-smart restoration and management strategies. Supplementary Information: The online version contains supplementary material available at 10.1007/s10533-024-01122-6.

Peatland restoration pathways to mitigate greenhouse gas emissions and retain peat carbon.

Peatlands play a crucial role in the global carbon (C) cycle, making their restoration a key strategy for mitigating greenhouse gas (GHG) emissions and retaining C. This study analyses the most common restoration pathways employed in boreal and temperate peatlands, potentially applicable in tropical peat swamp forests. Our analysis focuses on the GHG emissions and C retention potential of the restoration measures. To assess the C stock change in restored (rewetted) peatlands and afforested peatlands with continuous drainage, we adopt a conceptual approach that considers short-term C capture (GHG exchange between the atmosphere and the peatland ecosystem) and long-term C sequestration in peat. The primary criterion of our conceptual model is the capacity of restoration measures to capture C and reduce GHG emissions. Our findings indicate that carbon dioxide (CO2) is the most influential part of long-term climate impact of restored peatlands, whereas moderate methane (CH4) emissions and low N2O fluxes are relatively unimportant. However, lateral losses of dissolved and particulate C in water can account up to a half of the total C stock change. Among the restored peatland types, Sphagnum paludiculture showed the highest CO2 capture, followed by shallow lakes and reed/grass paludiculture. Shallow lakeshore vegetation in restored peatlands can reduce CO2 emissions and sequester C but still emit CH4, particularly during the first 20 years after restoration. Our conceptual modelling approach reveals that over a 300-year period, under stable climate conditions, drained bog forests can lose up to 50% of initial C content. In managed (regularly harvested) and continuously drained peatland forests, C accumulation in biomass and litter input does not compensate C losses from peat. In contrast, rewetted unmanaged peatland forests are turning into a persistent C sink. The modelling results emphasized the importance of long-term C balance analysis which considers soil C accumulation, moving beyond the short-term C cycling between vegetation and the atmosphere. Supplementary Information: The online version contains supplementary material available at 10.1007/s10533-023-01103-1.

Active afforestation of drained peatlands is not a viable option under the EU Nature Restoration Law.

The EU Nature Restoration Law (NRL) is critical for the restoration of degraded ecosystems and active afforestation of degraded peatlands has been suggested as a restoration measure under the NRL. Here, we discuss the current state of scientific evidence on the climate mitigation effects of peatlands under forestry. Afforestation of drained peatlands without restoring their hydrology does not fully restore ecosystem functions. Evidence on long-term climate benefits is lacking and it is unclear whether CO2 sequestration of forest on drained peatland can offset the carbon loss from the peat over the long-term. While afforestation may offer short-term gains in certain cases, it compromises the sustainability of peatland carbon storage. Thus, active afforestation of drained peatlands is not a viable option for climate mitigation under the EU Nature Restoration Law and might even impede future rewetting/restoration efforts. Instead, restoring hydrological conditions through rewetting is crucial for effective peatland restoration.

Substantial uptake of nitrous oxide (N2O) by shoots of mature European beech.

Similar to soils, tree stems emit and consume nitrous oxide (N2O) from the atmosphere. Although tree leaves dominate tree surface area, they have been completely excluded from field N2O flux measurements and therefore their role in forest N2O exchange remains unknown. We explored the contribution of leaf fluxes to forest N2O exchange. We determined the N2O exchange of mature European beech (Fagus sylvatica) stems and shoots (i.e., terminal branches) and of adjacent forest floor, in a typical temperate upland forest in Germany. The beech stems, and particularly the shoots, acted as net N2O sinks (-0.254 ± 0.827 µg N2O m-2 stem area h-1 and -4.54 ± 1.53 µg N2O m-2 leaf area h-1, respectively), while the forest floor was a net source (2.41 ± 1.08 µg N2O m-2 soil area h-1). The unstudied tree shoots were identified as a significant contributor to the net ecosystem N2O exchange. Moreover, we revealed for the first time that tree leaves act as substantial N2O sinks. Although this is the first study of its kind, it is of global importance for the proper design of future flux studies in forest ecosystems worldwide. Our results demonstrate that excluding tree leaves from forest N2O flux measurements can lead to misinterpretation of tree and forest N2O exchange, and thus global forest greenhouse gas flux inventories.

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.

Towards an integrated view on microbial CH4, N2O and N2 cycles in brackish coastal marsh soils: A comparative analysis of two sites.

Coastal ecosystems, facing threats from global change and human activities like excessive nutrients, undergo alterations impacting their function and appearance. This study explores the intertwined microbial cycles of carbon (C) and nitrogen (N), encompassing methane (CH4), nitrous oxide (N2O), and nitrogen gas (N2) fluxes, to determine nutrient transformation processes between the soil-plant-atmosphere continuum in the coastal ecosystems with brackish water. Water salinity negatively impacted denitrification, bacterial nitrification, N fixation, and n-DAMO processes, but did not significantly affect archaeal nitrification, COMAMMOX, DNRA, and ANAMMOX processes in the N cycle. Plant species age and biomass influenced CH4 and N2O emissions. The highest CH4 emissions were from old Spartina and mixed Spartina and Scirpus sites, while Phragmites sites emitted the most N2O. Nitrification and incomplete denitrification mainly governed N2O emissions depending on the environmental conditions and plants. The higher genetic potential of ANAMMOX reduced excessive N by converting it to N2 in the sites with higher average temperatures. The presence of plants led to a decrease in the N fixers' abundance. Plant biomass negatively affected methanogenetic mcrA genes. Microbes involved in n-DAMO processes helped mitigate CH4 emissions. Over 93 % of the total climate forcing came from CH4 emissions, except for the Chinese bare site where the climate forcing was negative, and for Phragmites sites, where almost 60 % of the climate forcing came from N2O emissions. Our findings indicate that nutrient cycles, CH4, and N2O fluxes in soils are context-dependent and influenced by environmental factors and vegetation. This underscores the need for empirical analysis of both C and N cycles at various levels (soil-plant-atmosphere) to understand how habitats or plants affect nutrient cycles and greenhouse gas emissions.

Connecting the multiple dimensions of global soil fungal diversity.

How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.

Global patterns in endemicity and vulnerability of soil fungi.

Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms.

Low water level drives high nitrous oxide emissions from treatment wetland.

Wetlands that are restored for carbon sequestration or created for water treatment are an important sources of greenhouse gases, especially methane. The emission of nitrous oxide (N2O) from these systems is often considered negligible due to the inundation and anerobic conditions that support complete denitrification. We used closed chamber method to analyze N2O fluxes over a long-term period across heterogeneous wetland ecosystem constructed for treating nitrate-rich agricultural runoff. Our results showed that the water depth and temperature were most important factors affecting high N2O emissions. The shallow areas where water depth was less than 9 cm created N2O hot spots that emitted 48.8% of the total wetlands annual emission while only covering 6% of the total area. The annual emission from shallow-water hot spots with dense helophytic vegetation was 4.85 ± 0.5 g N2O-N m-2 y-1 while it was only 0.37 ± 0.01 g N2O-N m-2 y-1 in deeper zones. While the water depth was the main factor for high N2O emissions, the temperatures increased the magnitude of the flux and therefore summer droughts and water drawdown created even larger hot spots. These results also suggest that IPCC benchmarks could underestimate N2O emission from shallow waterbodies. Thus, it is important that the shallow zones and water level drawdown in the created or restored wetlands is avoided to minimize the N2O flux.

Structure and function of the soil microbiome underlying N2O emissions from global wetlands.

Wetland soils are the greatest source of nitrous oxide (N2O), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the N2O emissions from wetland soils are poorly understood. Using in situ N2O measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and N2O emissions. We show that N2O emissions are higher in drained and warm wetland soils, and are correlated with functional diversity of microbes. We further provide evidence that despite their much lower abundance compared to bacteria, nitrifying archaeal abundance is a key factor explaining N2O emissions from wetland soils globally. Our data suggest that ongoing global warming and intensifying environmental change may boost archaeal nitrifiers, collectively transforming wetland soils to a greater source of N2O.

Does liming grasslands increase biomass productivity without causing detrimental impacts on net greenhouse gas emissions?

Soil acidification has negative impacts on grass biomass production and the potential of grasslands to mitigate greenhouse gas (GHG) emissions. Through a global review of research on liming of grasslands, the objective of this paper was to assess the impacts of liming on soil pH, grass biomass production and total net GHG exchange (nitrous oxide (N2O), methane (CH4) and net carbon dioxide (CO2)). We collected 57 studies carried out at 88 sites and covering different countries and climatic zones. All of the studies examined showed that liming either reduced or had no effects on the emissions of two potent greenhouse gases (N2O and CH4). Though liming of grasslands can increase net CO2 emissions, the impact on total net GHG emission is minimal due to the higher global warming potential, over a 100-year period, of N2O and CH4 compared to that of CO2. Liming grassland delivers many potential advantages, which justify its wider adoption. It significantly ameliorates soil acidity, increases grass productivity, reduces fertiliser requirement and increases species richness. To realise the maximum benefit of liming grassland, we suggest that acidic soils should be moderately limed within the context of specific climates, soils and management.

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.

Restoring wetlands on intensive agricultural lands modifies nitrogen cycling microbial communities and reduces N2O production potential.

The concentration of nitrous oxide (N2O), an ozone-depleting greenhouse gas, is rapidly increasing in the atmosphere. Most atmospheric N2O originates in terrestrial ecosystems, of which the majority can be attributed to microbial cycling of nitrogen in agricultural soils. Here, we demonstrate how the abundance of nitrogen cycling genes vary across intensively managed agricultural fields and adjacent restored wetlands in the Sacramento-San Joaquin Delta in California, USA. We found that the abundances of nirS and nirK genes were highest at the intensively managed organic-rich cornfield and significantly outnumber any other gene abundances, suggesting very high N2O production potential. The quantity of nitrogen transforming genes, particularly those responsible for denitrification, nitrification and DNRA, were highest in the agricultural sites, whereas nitrogen fixation and ANAMMOX was strongly associated with the wetland sites. Although the abundance of nosZ genes was also high at the agricultural sites, the ratio of nosZ genes to nir genes was significantly higher in wetland sites indicating that these sites could act as a sink of N2O. These findings suggest that wetland restoration could be a promising natural climate solution not only for carbon sequestration but also for reduced N2O emissions.

High denitrification potential but low nitrous oxide emission in a constructed wetland treating nitrate-polluted agricultural run-off.

Constructed wetlands (CW) can efficiently remove nitrogen from polluted agricultural run-off, however, a potential caveat is nitrous oxide (N2O), a harmful greenhouse gas and stratospheric ozone depleter. During five sampling campaigns, we measured N2O fluxes from a 0.53 ha off-stream CW treating nitrate-rich water from the intensively fertilized watershed in Rampillon, France, using automated chambers with a quantum cascade laser system, and manual chambers. Sediment samples were analysed for potential N2 flux using the HeO2 incubation method. Both inlet nitrate (NO3-) concentrations and N2O emission varied significantly between the seasons. In the Autumn and Winter inlet concentrations were about 11 mg NO3--N L-1, and < 6.5 mg NO3--N L-1 in the Spring and Summer. N2O emission was highest in the Autumn (mean ± standard error: 9.7 ± 0.2 µg N m-2 h-1) and lowest in the Summer (wet period: 0.2 ± 0.3 µg N m-2 h-1). The CW was a very weak source of N2O emitting 0.32 kg N2O-N ha-1 yr-1 and removing around 938 kg NO3--N ha-1 yr-1, the ratio of N2O-N emitted to NO3--N removed was 0.033%. The automated and manual chambers gave similar results. From the potential N2O formation in the sediment, only 9% was emitted to the atmosphere, the average N2 N 2O ratio was high: 89:1 for N2-Npotential: N2O-Npotential and 1353:1 for N2-Npotential: N2O-Nemitted. These results indicate complete denitrification. The focused principal component analysis showed strong positive correlation between the gaseous N2O fluxes and the following environmental factors: NO3--N concentrations in inlet water, streamflow, and nitrate reduction rate. Water temperature, TOC and DOC in the water and hydraulic residence time showed negative correlations with N2O emissions. Shallow off-stream CWs such as Rampillon may have good nitrate removal capacity with low N2O emissions.

Temperature and pH define the realised niche space of arbuscular mycorrhizal fungi.

The arbuscular mycorrhizal (AM) fungi are a globally distributed group of soil organisms that play critical roles in ecosystem function. However, the ecological niches of individual AM fungal taxa are poorly understood. We collected > 300 soil samples from natural ecosystems worldwide and modelled the realised niches of AM fungal virtual taxa (VT; approximately species-level phylogroups). We found that environmental and spatial variables jointly explained VT distribution worldwide, with temperature and pH being the most important abiotic drivers, and spatial effects generally occurring at local to regional scales. While dispersal limitation could explain some variation in VT distribution, VT relative abundance was almost exclusively driven by environmental variables. Several environmental and spatial effects on VT distribution and relative abundance were correlated with phylogeny, indicating that closely related VT exhibit similar niche optima and widths. Major clades within the Glomeraceae exhibited distinct niche optima, Acaulosporaceae generally had niche optima in low pH and low temperature conditions, and Gigasporaceae generally had niche optima in high precipitation conditions. Identification of the realised niche space occupied by individual and phylogenetic groups of soil microbial taxa provides a basis for building detailed hypotheses about how soil communities respond to gradients and manipulation in ecosystems worldwide.

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.

Mapping the field of constructed wetland-microbial fuel cell: A review and bibliometric analysis.

The embedding microbial fuel cell (MFC) into constructed wetlands (CW) to form CW-MFC bears the potential to obtain bioelectricity and a clean environment. In this study, a bibliometric analysis using VOSviewer based on Web of Science data was conducted to provide an overview by tracing the development footprint of this technology. The countries, institutions, authors, key terms, and keywords were tracked and corresponding mapping was generated. From 2012 to September 2020, 442 authors from 129 organizations in 26 countries published 135 publications in 42 journals with total citation of 3139 times were found. The key terms analysis showed four clusters: bioelectricity generation performance, mechanism study, refractory pollutants removal, and enhanced conventional contaminants removal. Further research themes include exploring the biochemical properties of electrochemically active bacteria, emerging contaminants removal, effective bioelectricity harvest and the use, and biosensor development as well as scaling-up for real field application. The bibliometric results provide valuable references and information on potential research directions for future studies.

Soil Bacterial and Archaeal Communities and Their Potential to Perform N-Cycling Processes in Soils of Boreal Forests Growing on Well-Drained Peat.

Peatlands are unique wetland ecosystems that cover approximately 3% of the world's land area and are mostly located in boreal and temperate regions. Around 15 Mha of these peatlands have been drained for forestry during the last century. This study investigated soil archaeal and bacterial community structure and abundance, as well as the abundance of marker genes of nitrogen transformation processes (nitrogen fixation, nitrification, denitrification, and dissimilatory nitrate reduction to ammonia) across distance gradients from drainage ditches in nine full-drained, middle-aged peatland forests dominated by Scots pine, Norway spruce, or Downy birch. The dominating tree species had a strong effect on the chemical properties (pH, N and C/N status) of initially similar Histosols and affected the bacterial and archaeal community structure and abundance of microbial groups involved in the soil nitrogen cycle. The pine forests were distinguished by having the lowest fine root biomass of trees, pH, and N content and the highest potential for N fixation. The distance from drainage ditches affected the spatial distribution of bacterial and archaeal communities (especially N-fixers, nitrifiers, and denitrifiers possessing nosZ clade II), but this effect was often dependent on the conditions created by the dominance of certain tree species. The composition of the nitrifying microbial community was dependent on the soil pH, and comammox bacteria contributed significantly to nitrate formation in the birch and spruce soils where the pH was higher than 4.6. The highest N2O emission was recorded from soils with higher bacterial and archaeal phylogenetic diversity such as birch forest soils. This study demonstrates that the long-term growth of forests dominated by birch, pine, and spruce on initially similar organic soil has resulted in tree-species-specific changes in the soil properties and the development of forest-type-specific soil prokaryotic communities with characteristic functional properties and relationships within microbial communities.

Increasing fragmentation of forest cover in Brazil's Legal Amazon from 2001 to 2017.

Persistent forest loss in the Brazilian Legal Amazon (BLA) is responsible for carbon emission, reduction of ecosystem services, and loss of biodiversity. Combining spatial data analysis with high spatial resolution data for forest cover and forest loss, we quantified the spatial and temporal patterns of forest dynamics in the BLA. We identified an alarming trend of increasing deforestation, with especially high rates in 2016 and 2017. Moreover, the creation of forest cover fragments is faster than ever due to decreasing size and dispersion of forest loss patches. From 2001 to 2017, the number of large forest loss patches decreased significantly, accompanied by a reduction in the size of these patches. Enforcement of field inspections and of initiatives to promote forest conservation will be required to stop this trend.

Short-term flooding increases CH4 and N2O emissions from trees in a riparian forest soil-stem continuum.

One of the characteristics of global climate change is the increase in extreme climate events, e.g., droughts and floods. Forest adaptation strategies to extreme climate events are the key to predict ecosystem responses to global change. Severe floods alter the hydrological regime of an ecosystem which influences biochemical processes that control greenhouse gas fluxes. We conducted a flooding experiment in a mature grey alder (Alnus incana (L.) Moench) forest to understand flux dynamics in the soil-tree-atmosphere continuum related to ecosystem N2O and CH4 turn-over. The gas exchange was determined at adjacent soil-tree-pairs: stem fluxes were measured in vertical profiles using manual static chambers and gas chromatography; soil fluxes were measured with automated chambers connected to a gas analyser. The tree stems and soil surface were net sources of N2O and CH4 during the flooding. Contrary to N2O, the increase in CH4 fluxes delayed in response to flooding. Stem N2O fluxes were lower although stem CH4 emissions were significantly higher than from soil after the flooding. Stem fluxes decreased with stem height. Our flooding experiment indicated soil water and nitrogen content as the main controlling factors of stem and soil N2O fluxes. The stems contributed up to 88% of CH4 emissions to the stem-soil continuum during the investigated period but soil N2O fluxes dominated (up to 16 times the stem fluxes) during all periods. Conclusively, stem fluxes of CH4 and N2O are essential elements in forest carbon and nitrogen cycles and must be included in relevant models.