Tracing State Structure for Ecological Processes in Soil Including Greenhouse Gas Exchange with Lower Atmosphere.

Exploring data aids in the comprehension of the dataset and the system's essence. Various approaches exist for managing numerous sensors. This study perceives operational states to clarify the physical dynamics within a soil environment. Utilizing Principal Component Analysis (PCA) enables dimensionality reduction, offering an alternative perspective on the spring soil dataset. The K-means algorithm clusters data densities, forming the groundwork for an operational state description. Soil data, integral to an ecosystem, entails evident attributes. Employing dynamic visualization, including animations, constitutes a vital exploration angle. Greenhouse gas variables have been added to PCA to achieve more understanding in the interconnection of gas exchange and soil properties. Pit data and flux data are analysed both separately and together using a data-driven approach. The results look promising, showing the potential to add new values and more detailed state structures to ecological models. All experiments are conducted within the Jupyter programming environment, utilizing Python 3. The relevant literature on data visualization is examined. Through combined techniques and tools, the potential features of the soil ecosystem are observed and identified.

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.

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.

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.

Ligneous amendments increase soil organic carbon content in fine-textured boreal soils and modulate N2O emissions.

Organic soil amendments are used to improve soil quality and mitigate climate change. However, their effects on soil structure, nutrient and water retention as well as greenhouse gas (GHG) emissions are still poorly understood. The purpose of this study was to determine the residual effects of a single field application of four ligneous soil amendments on soil structure and GHG emissions. We conducted a laboratory incubation experiment using soil samples collected from an ongoing soil-amendment field experiment at Qvidja Farm in south-west Finland, two years after a single application of four ligneous biomasses. Specifically, two biochars (willow and spruce) produced via slow pyrolysis, and two mixed pulp sludges from paper industry side-streams were applied at a rate of 9-22 Mg ha-1 mixed in the top 0.1 m soil layer. An unamended fertilized soil was used as a control. The laboratory incubation lasted for 33 days, during which the samples were kept at room temperature (21°C) and at 20%, 40%, 70% or 100% water holding capacity. Carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4) fluxes were measured periodically after 1, 5, 12, 20 and 33 days of incubation. The application of ligneous soil amendments increased the pH of the sampled soils by 0.4-0.8 units, whereas the effects on soil organic carbon content and soil structure varied between treatments. The GHG exchange was dominated by CO2 emissions, which were mainly unaffected by the soil amendment treatments. The contribution of soil CH4 exchange was negligible (nearly no emissions) compared to soil CO2 and N2O emissions. The soil N2O emissions exhibited a positive exponential relationship with soil moisture. Overall, the soil amendments reduced N2O emissions on average by 13%, 64%, 28%, and 37%, at the four soil moisture levels, respectively. Furthermore, the variation in N2O emissions between the amendments correlated positively with their liming effect. More specifically, the potential for the pulp sludge treatments to modulate N2O emissions was evident only in response to high water contents. This tendency to modulate N2O emissions was attributed to their capacity to increase soil pH and influence soil processes by persisting in the soil long after their application.

Soil GHG dynamics after water level rise - Impacts of selection harvesting in peatland forests.

Managed boreal peatlands are widespread and economically important, but they are a large source of greenhouse gases (GHGs). Peatland GHG emissions are related to soil water-table level (WT), which controls the vertical distribution of aerobic and anaerobic processes and, consequently, sinks and sources of GHGs in soils. On forested peatlands, selection harvesting reduces stand evapotranspiration and it has been suggested that the resulting WT rise decreases soil net emissions, while the tree growth is maintained. We monitored soil concentrations of CO2, CH4, N2O and O2 by depth down to 80 cm, and CO2 and CH4 fluxes from soil in two nutrient-rich Norway spruce dominated peatlands in Southern Finland to examine the responses of soil GHG dynamics to WT rise. Selection harvesting raised WT by 14 cm on both sites, on average, mean WTs of the monitoring period being 73 cm for unharvested control and 59 cm for selection harvest. All soil gas concentrations were associated with proximity to WT. Both CH4 and CO2 showed remarkable vertical concentration gradients, with high values in the deepest layer, likely due to slow gas transfer in wet peat. CH4 was efficiently consumed in peat layers near and above WT where it reached sub-atmospheric concentrations, indicating sustained oxidation of CH4 from both atmospheric and deeper soil origins also after harvesting. Based on soil gas concentration data, surface peat (top 25/30 cm layer) contributed most to the soil-atmosphere CO2 fluxes and harvesting slightly increased the CO2 source in deeper soil (below 45/50 cm), which could explain the small CO2 flux differences between treatments. N2O production occurred above WT, and it was unaffected by harvesting. Overall, the WT rise obtained with selection harvesting was not sufficient to reduce soil GHG emissions, but additional hydrological regulation would have been needed.

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.

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.

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.

Global Research Alliance N2 O chamber methodology guidelines: Design considerations.

Terrestrial ecosystems, both natural ecosystems and agroecosystems, generate greenhouse gases (GHGs). The chamber method is the most common method to quantify GHG fluxes from soil-plant systems and to better understand factors affecting their generation and mitigation. The objective of this study was to review and synthesize literature on chamber designs (non-flow-through, non-steady-state chamber) and associated factors that affect GHG nitrous oxide (N2 O) flux measurement when using chamber methods. Chamber design requires consideration of many facets that include materials, insulation, sealing, venting, depth of placement, and the need to maintain plant growth and activity. Final designs should be tailored, and bench tested, in order to meet the nuances of the experimental objectives and the ecosystem under study while reducing potential artifacts. Good insulation, to prevent temperature fluctuations and pressure changes, and a high-quality seal between base and chamber are essential. Elimination of pressure differentials between headspace and atmosphere through venting should be performed, and designs now exist to eliminate Venturi effects of earlier tube-type vent designs. The use of fans within the chamber headspace increases measurement precision but may alter the flux. To establish best practice recommendations when using fans, further data are required, particularly in systems containing tall plants, to systematically evaluate the effects that fan speed, position, and mixing rate have on soil gas flux.

Author Correction: Neglecting diurnal variations leads to uncertainties in terrestrial nitrous oxide emissions.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Seasonal dynamics of stem N2O exchange follow the physiological activity of boreal trees.

The role of trees in the nitrous oxide (N2O) balance of boreal forests has been neglected despite evidence suggesting their substantial contribution. We measured seasonal changes in N2O fluxes from soil and stems of boreal trees in Finland, showing clear seasonality in stem N2O flux following tree physiological activity, particularly processes of CO2 uptake and release. Stem N2O emissions peak during the vegetation season, decrease rapidly in October, and remain low but significant to the annual totals during winter dormancy. Trees growing on dry soils even turn to consumption of N2O from the atmosphere during dormancy, thereby reducing their overall N2O emissions. At an annual scale, pine, spruce and birch are net N2O sources, with spruce being the strongest emitter. Boreal trees thus markedly contribute to the seasonal dynamics of ecosystem N2O exchange, and their species-specific contribution should be included into forest emission inventories.

Plant roots increase both decomposition and stable organic matter formation in boreal forest soil.

Boreal forests are ecosystems with low nitrogen (N) availability that store globally significant amounts of carbon (C), mainly in plant biomass and soil organic matter (SOM). Although crucial for future climate change predictions, the mechanisms controlling boreal C and N pools are not well understood. Here, using a three-year field experiment, we compare SOM decomposition and stabilization in the presence of roots, with exclusion of roots but presence of fungal hyphae and with exclusion of both roots and fungal hyphae. Roots accelerate SOM decomposition compared to the root exclusion treatments, but also promote a different soil N economy with higher concentrations of organic soil N compared to inorganic soil N accompanied with the build-up of stable SOM-N. In contrast, root exclusion leads to an inorganic soil N economy (i.e., high level of inorganic N) with reduced stable SOM-N build-up. Based on our findings, we provide a framework on how plant roots affect SOM decomposition and stabilization.

Interannual and Seasonal Dynamics of Volatile Organic Compound Fluxes From the Boreal Forest Floor.

In the northern hemisphere, boreal forests are a major source of biogenic volatile organic compounds (BVOCs), which drive atmospheric processes and lead to cloud formation and changes in the Earth's radiation budget. Although forest vegetation is known to be a significant source of BVOCs, the role of soil and the forest floor, and especially interannual variations in fluxes, remains largely unknown due to a lack of long-term measurements. Our aim was to determine the interannual, seasonal and diurnal dynamics of boreal forest floor volatile organic compound (VOC) fluxes and to estimate how much they contribute to ecosystem VOC fluxes. We present here an 8-year data set of forest floor VOC fluxes, measured with three automated chambers connected to the quadrupole proton transfer reaction mass spectrometer (quadrupole PTR-MS). The exceptionally long data set shows that forest floor fluxes were dominated by monoterpenes and methanol, with relatively comparable emission rates between the years. Weekly mean monoterpene fluxes from the forest floor were highest in spring and in autumn (maximum 59 and 86 µg m-2 h-1, respectively), whereas the oxygenated VOC fluxes such as methanol had highest weekly mean fluxes in spring and summer (maximum 24 and 79 µg m-2 h-1, respectively). Although the chamber locations differed from each other in emission rates, the inter-annual dynamics were very similar and systematic. Accounting for this chamber location dependent variability, temperature and relative humidity, a mixed effects linear model was able to explain 79-88% of monoterpene, methanol, acetone, and acetaldehyde fluxes from the boreal forest floor. The boreal forest floor was a significant contributor in the forest stand fluxes, but its importance varies between seasons, being most important in autumn. The forest floor emitted 2-93% of monoterpene fluxes in spring and autumn and 1-72% of methanol fluxes in spring and early summer. The forest floor covered only a few percent of the forest stand fluxes in summer.

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

Tree stems from wetland, floodplain and upland forests can produce and emit methane (CH4 ). Tree CH4 stem emissions have high spatial and temporal variability, but there is no consensus on the biophysical mechanisms that drive stem CH4 production and emissions. Here, we summarize up to 30 opportunities and challenges for stem CH4 emissions research, which, when addressed, will improve estimates of the magnitudes, patterns and drivers of CH4 emissions and trace their potential origin. We identified the need: (1) for both long-term, high-frequency measurements of stem CH4 emissions to understand the fine-scale processes, alongside rapid large-scale measurements designed to understand the variability across individuals, species and ecosystems; (2) to identify microorganisms and biogeochemical pathways associated with CH4 production; and (3) to develop a mechanistic model including passive and active transport of CH4 from the soil-tree-atmosphere continuum. Addressing these challenges will help to constrain the magnitudes and patterns of CH4 emissions, and allow for the integration of pathways and mechanisms of CH4 production and emissions into process-based models. These advances will facilitate the upscaling of stem CH4 emissions to the ecosystem level and quantify the role of stem CH4 emissions for the local to global CH4 budget.

Neglecting diurnal variations leads to uncertainties in terrestrial nitrous oxide emissions.

Nitrous oxide (N2O) is an important greenhouse gas produced in soil and aquatic ecosystems. Its warming potential is 296 times higher than that of CO2. Most N2O emission measurements made so far are limited in temporal and spatial resolution causing uncertainties in the global N2O budget. Recent advances in laser spectroscopic techniques provide an excellent tool for area-integrated, direct and continuous field measurements of N2O fluxes using the eddy covariance method. By employing this technique on an agricultural site with four laser-based analysers, we show here that N2O exchange exhibits contrasting diurnal behaviour depending upon soil nitrogen availability. When soil N was high due to fertilizer application, N2O emissions were higher during daytime than during the night. However, when soil N became limited, emissions were higher during the night than during the day. These reverse diurnal patterns supported by isotopic analyses may indicate a dominant role of plants on microbial processes associated with N2O exchange. This study highlights the potential of new technologies in improving estimates of global N2O sources.

Pinus sylvestris as a missing source of nitrous oxide and methane in boreal forest.

Boreal forests comprise 73% of the world's coniferous forests. Based on forest floor measurements, they have been considered a significant natural sink of methane (CH4) and a natural source of nitrous oxide (N2O), both of which are important greenhouse gases. However, the role of trees, especially conifers, in ecosystem N2O and CH4 exchange is only poorly understood. We show for the first time that mature Scots pine (Pinus sylvestris L.) trees consistently emit N2O and CH4 from both stems and shoots. The shoot fluxes of N2O and CH4 exceeded the stem flux rates by 16 and 41 times, respectively. Moreover, higher stem N2O and CH4 fluxes were observed from wet than from dry areas of the forest. The N2O release from boreal pine forests may thus be underestimated and the uptake of CH4 may be overestimated when ecosystem flux calculations are based solely on forest floor measurements. The contribution of pine trees to the N2O and CH4 exchange of the boreal pine forest seems to increase considerably under high soil water content, thus highlighting the urgent need to include tree-emissions in greenhouse gas emission inventories.

Micrometeorological measurements of methane and carbon dioxide fluxes at a municipal landfill.

Continuous and area-integrating monitoring of methane (CH4) and carbon dioxide (CO2) emissions was performed for 6 and 9 months, respectively, at a municipal landfill in Finland with the micrometeorological eddy covariance (EC) method. The mean CH4 emission from June to December was 0.53 mg m(-2) s(-1), while the CO2 emission between February and December averaged 1.78 mg m(-2) s(-1). The CH4 emissions from the summit area of the landfill, where active waste deposition was going on, were 1.7 times as high as from the slope area with a better surface cover. The variation in emissions over the source area of the measurement was high. Significant seasonal variation, linked to air and soil temperature, was only seen in the CO2 release rates. Results obtained with the EC method were comparable to those measured with closed static chambers. According to the EC measurements, the gas recovery system decreased CH4 fluxes by 69-79%. The ratio of the measured CH4 and CO2 emissions roughly indicated the route of the landfill gas emission, resembling the ratio of the gases measured in the gas wells (1.24) when the emission originated from the area with no oxidizing cover layer and being smaller when CH4 oxidation had taken place.