Browsing by Subject "RESPIRATION"

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  • Ouwerkerk, Janneke P.; van der Ark, Kees C. H.; Davids, Mark; Claassens, Nico J.; Finestra, Teresa Robert; de Vos, Willem M.; Belzer, Clara (2016)
    Akkermansia muciniphila colonizes the mucus layer of the gastrointestinal tract, where the organism can be exposed to the oxygen that diffuses from epithelial cells. To understand how A. muciniphila is able to survive and grow at this oxic-anoxic interface, its oxygen tolerance and response and reduction capacities were studied. A. muciniphila was found to be oxygen tolerant. On top of this, under aerated conditions, A. muciniphila showed significant oxygen reduction capacities and its growth rate and yield were increased compared to those seen under strict anaerobic conditions. Transcriptome analysis revealed an initial oxygen stress response upon exposure to oxygen. Thereafter, genes related to respiration were expressed, including those coding for the cytochrome bd complex, which can function as a terminal oxidase. The functionality of A. muciniphila cytochrome bd genes was proven by successfully complementing cytochrome-deficient Escherichia coli strain ECOM4. We conclude that A. muciniphila can use oxygen when it is present at nanomolar concentrations. IMPORTANCE This article explains how Akkermansia muciniphila, previously described as a strictly anaerobic bacterium, is able to tolerate and even benefit from low levels of oxygen. Interestingly, we measured growth enhancement of A. muciniphila and changes in metabolism as a result of the oxygen exposure. In this article, we discuss similarities and differences of this oxygen-responsive mechanism with respect to those of other intestinal anaerobic isolates. Taken together, we think that these are valuable data that indicate how anaerobic intestinal colonizing bacteria can exploit low levels of oxygen present in the mucus layer and that our results have direct relevance for applicability, as addition of low oxygen concentrations could benefit the in vitro growth of certain anaerobic organisms.
  • Minunno, Francesco; Peltoniemi, Mikko; Harkonen, Sanna; Kalliokoski, Tuomo; Makinen, Harri; Makela, Annikki (2019)
    Policy-relevant forest models must be environment and management sensitive and provide unbiased estimates of predicted variables over their intended areas of application. While empirical models derive their structure and parameters from representative data sets, process-based model (PBM) parameters should be evaluated in ranges that have a biological meaning independently of output data. At the same time PBMs should be calibrated against observations in order to obtain unbiased estimates and an understanding of their predictive capability. By means of model data assimilation, we Bayesian calibrated a forest model (PREBAS) using an extensive dataset that covered a wide range of climatic conditions, species composition and management practices. PREBAS was calibrated for three species in Finland: Scots pine (Pinus sylvestris L.), Norway spruce (Picea abies [L.] H. Karst.) and Silver birch (Betula pendula L.). Data assimilation was strongly effective in reducing the uncertainty of PREBAS parameters and predictions. A country-generic calibration showed robust performances in predicting forest variables and the results were consistent with yield tables and national forest statistics. The posterior predictive uncertainty of the model was mainly influenced by the uncertainty of the structural and measurement error.
  • Flechard, Chris R.; van Oijen, Marcel; Cameron, David R.; de Vries, Wim; Ibrom, Andreas; Buchmann, Nina; Dise, Nancy B.; Janssens, Ivan A.; Neirynck, Johan; Montagnani, Leonardo; Varlagin, Andrej; Loustau, Denis; Legout, Arnaud; Ziemblinska, Klaudia; Aubinet, Marc; Aurela, Mika; Chojnicki, Bogdan H.; Drewer, Julia; Eugster, Werner; Francez, Andre-Jean; Juszczak, Radoslaw; Kitzler, Barbara; Kutsch, Werner L.; Lohila, Annalea; Longdoz, Bernard; Matteucci, Giorgio; Moreaux, Virginie; Nefte, Albrecht; Olejnik, Janusz; Sanz, Maria J.; Siemens, Jan; Vesala, Timo; Vincke, Caroline; Nemitz, Eiko; Zechmeister-Boltenstern, Sophie; Butterbach-Bahl, Klaus; Skiba, Ute M.; Sutton, Mark A. (2020)
    The effects of atmospheric nitrogen deposition (N-dep) on carbon (C) sequestration in forests have often been assessed by relating differences in productivity to spatial variations of N-dep across a large geographic domain. These correlations generally suffer from covariation of other confounding variables related to climate and other growth-limiting factors, as well as large uncertainties in total (dry + wet) reactive nitrogen (N-r) deposition. We propose a methodology for untangling the effects of N-dep from those of meteorological variables, soil water retention capacity and stand age, using a mechanistic forest growth model in combination with eddy covariance CO2 exchange fluxes from a Europe-wide network of 22 forest flux towers. Total N-r deposition rates were estimated from local measurements as far as possible. The forest data were compared with data from natural or semi-natural, non-woody vegetation sites. The response of forest net ecosystem productivity to nitrogen deposition (dNEP/dN(dep)) was estimated after accounting for the effects on gross primary productivity (GPP) of the co-correlates by means of a meta-modelling standardization procedure, which resulted in a reduction by a factor of about 2 of the uncorrected, apparent dGPP/dN(dep) value. This model-enhanced analysis of the C and N-dep flux observations at the scale of the European network suggests a mean overall dNEP/dN(dep) response of forest lifetime C sequestration to N-dep of the order of 40-50 g C per g N, which is slightly larger but not significantly different from the range of estimates published in the most recent reviews. Importantly, patterns of gross primary and net ecosystem productivity versus N-dep were non-linear, with no further growth responses at high N-dep levels (N-dep > 2.5-3 gNm(-2) yr(-1)) but accompanied by increasingly large ecosystem N losses by leaching and gaseous emissions. The reduced increase in productivity per unit N deposited at high N-dep levels implies that the forecast increased N-r emissions and increased N-dep levels in large areas of Asia may not positively impact the continent's forest CO2 sink. The large level of unexplained variability in observed carbon sequestration efficiency (CSE) across sites further adds to the uncertainty in the dC/dN response.
  • Koster, Kajar; Koster, Egle; Berninger, Frank; Heinonsalo, Jussi; Pumpanen, Jukka (2018)
    Reindeer (Rangifer tarandus L.) is considered to be an important mammalian herbivore, strongly influencing Arctic lichen-dominated ecosystems. There is no wide knowledge about the effect of reindeer on greenhouse gas (GHG) fluxes in northern boreal forests. Ground vegetation plays an important role in absorbing nitrogen (N) and carbon dioxide (CO2) from the atmosphere. Lately, it has also been found to be a significant source of nitrous oxide (N2O) and a small source of methane (CH4). We investigated the influence of reindeer grazing on field layer GHG (CO2, CH4, and N2O) fluxes, ground vegetation coverage and biomass, and soil physical properties (temperature and moisture) in a northern boreal forest. At our study site, the reindeer-induced replacement of lichen by mosses had contrasting effects on the GHG fluxes originating from the field layer. Field layer CO2 efflux was significantly higher in grazed areas. The field layer was a CH4 sink in all areas, but grazed areas absorbed more CH4 compared to non-grazed areas. Although total N2O fluxes remained around 0 in grazed areas, a small N2O sink occurred in non-grazed areas with lower moss biomass. Our results indicated that grazing by reindeer in northern boreal forests affects GHG fluxes from the forest field layer both positively and negatively, and these emissions largely depend on grazing-induced changes in vegetation composition.
  • Ojanen, Paavo; Mäkiranta, Päivi; Penttilä, Timo; Minkkinen, Kari (2017)
    Logging residue piles have been suggested to markedly increase the decomposition of the underlying peat soil leading to large carbon dioxide emissions. We aimed at scrutinizing this postulate with straightforward decomposition (mass loss) measurements. For the purpose, authentic soil organic matter (humus and peat) was incubated in mesh bags under piles and at control plots. The effect of piles was assumed to result from physical (shading and insulation on soil surface) and chemical-biological (leaching of nutrients and fresh organic matter) sources. To distinguish between the two, artificial piles of inorganic matter were established to mimic the bare physical effects. Enhancement of decomposition in the soil under the real and artificial piles was assessed by measuring the mass loss of cellulose strips. Logging residue piles had clear physical effects on soil: temperatures were lowered and their diurnal variation subdued, and relative humidity at the soil surface was higher. The effect on soil moisture was also evident, but more variable, including both decreases and increases. These effects, mimicked by the artificial piles, decreased rather than increased cellulose mass loss. As the real piles, on the other hand, increased mass loss, we conclude that logging residue piles may enhance decomposition in soil due to chemical-biological mechanisms. Also the results on humus and peat mass loss indicate that piles can both increase and decrease decomposition. Consistent, remarkable increase in mass loss was not observed. Thus, our results do not support the postulate of logging residue piles dramatically increasing decomposition of soil organic matter. Rather, they hint that the effect of logging residue piles on soil is an interplay of physical and chemical-biological effects and carbon transport via roots and fungi. To fully understand and quantify these effects, vertical C fluxes between piles and soil and horizontal C fluxes within soil need to be assessed in addition to decomposition in soil and piles.
  • Lindroth, Anders; Holst, Jutta; Linderson, Maj-Lena; Aurela, Mika; Biermann, Tobias; Heliasz, Michal; Chi, Jinshu; Ibrom, Andreas; Kolari, Pasi; Klemedtsson, Leif; Krasnova, Alisa; Laurila, Tuomas; Lehner, Irene; Lohila, Annalea; Mammarella, Ivan; Mölder, Meelis; Lofvenius, Mikaell Ottosson; Peichl, Matthias; Pilegaard, Kim; Soosaar, Kaido; Vesala, Timo; Vestin, Patrik; Weslien, Per; Nilsson, Mats (2020)
    The Nordic region was subjected to severe drought in 2018 with a particularly long-lasting and large soil water deficit in Denmark, Southern Sweden and Estonia. Here, we analyse the impact of the drought on carbon and water fluxes in 11 forest ecosystems of different composition: spruce, pine, mixed and deciduous. We assess the impact of drought on fluxes by estimating the difference (anomaly) between year 2018 and a reference year without drought. Unexpectedly, the evaporation was only slightly reduced during 2018 compared to the reference year at two sites while it increased or was nearly unchanged at all other sites. This occurred under a 40 to 60% reduction in mean surface conductance and the concurrent increase in evaporative demand due to the warm and dry weather. The anomaly in the net ecosystem productivity (NEP) was 93% explained by a multilinear regression with the anomaly in heterotrophic respiration and the relative precipitation deficit as independent variables. Most of the variation (77%) was explained by the heterotrophic component. Six out of 11 forests reduced their annual NEP with more than 50 g C m(-2)yr(-1)during 2018 as compared to the reference year. The NEP anomaly ranged between -389 and +74 g C m(-2)yr(-1)with a median value of -59 g C m(-2)yr(-1). This article is part of the theme issue 'Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale'.
  • Gammal, Johanna; Järnström, Marie; Bernard, Guillaume; Norkko, Joanna; Norkko, Alf (2019)
    The ongoing loss of biodiversity and global environmental changes severely affect the structure of coastal ecosystems. Consequences, in terms of ecosystem functioning, are, however, difficult to predict because the context dependency of the biodiversity-ecosystem function relationships within these heterogeneous seascapes is poorly understood. To assess the effects of biological and environmental factors in mediating ecosystem functioning (nutrient cycling) in different natural habitats, intact sediment cores were collected at 18 sites on a grain size gradient from coarse sand to silt, with varying organic matter content and vegetation. To assess ecosystem functioning, solute fluxes (O-2, NH4+, PO43-, Si) across the sediment-water interface were measured. The macrofaunal communities changed along the grain size gradient with higher abundance, biomass and number of species in coarser sediments and in habitats with more vegetation. Across the whole gradient, the macrofauna cumulatively accounted for 25% of the variability in the multivariate solute fluxes, whereas environmental variables cumulatively accounted for 20%. Only the biomass and abundance of a few of the most dominant macrofauna species, not the number of species, appeared to contribute significantly to the nutrient recycling processes. Closer analyses of different sediment types (grouped into coarse, medium and fine sediment) showed that the macrofauna was an important predictor in all sediment types, but had the largest impact in fine and medium sediments. The results imply that even if the ecosystem functioning is similar in different sediment types, the underpinning mechanisms are different, which makes it challenging to generalize patterns of functioning across the heterogeneous shallow coastal zones.
  • Silva, Luis; Calleja, Maria Ll.; Ivetic, Snjezana; Huete-Stauffer, Tamara; Roth, Florian; Carvalho, Susana; Moran, Xose Anxelu G. (2021)
    In coral reefs, dissolved organic matter (DOM) cycling is a critical process for sustaining ecosystem functioning. However, global and local stressors have caused persistent shifts from coral- to algae-dominated benthic communities. The influence of such phase shifts on DOM nature and its utilization by heterotrophic bacterioplankton remains poorly studied. Every second month for one year, we retrieved seawater samples enriched in DOM produced by coral- and algae-dominated benthic communities in a central Red Sea reef during a full annual cycle. Seawater incubations were conducted in the laboratory under in situ temperature and light conditions by inoculating enriched DOM samples with bacterial assemblages collected in the surrounding waters. Dissolved organic carbon (DOC) concentrations were higher in the warmer months (May-September) in both communities, resulting in higher specific growth rates and bacterial growth efficiencies (BGE). However, these high summer values were significantly enhanced in algal-DOM relative to coral-DOM, suggesting the potential for bacterioplankton biomass increase in reefs with algae replacing healthy coral cover under warmer conditions. The potential exacerbation of heterotrophic bacterial activity in the ongoing widespread regime shift from coral- to algae-dominated communities may have detrimental consequences for the overall health of tropical coral reefs. (C) 2020 The Authors. Published by Elsevier B.V.
  • Kittler, Fanny; Eugster, Werner; Foken, Thomas; Heimann, Martin; Kolle, Olaf; Göckede, Mathias (2017)
    This study aimed at quantifying potential negative effects of instrument heating to improve eddy-covariance flux data quality in cold environments. Our overarching objective was to minimize heating-related bias in annual CO2 budgets from an Arctic permafrost system. We used continuous eddy-covariance measurements covering three full years within an Arctic permafrost ecosystem with parallel sonic anemometers operation with activated heating and without heating as well as parallel operation of open- and closed-path gas analyzers, the latter serving as a reference. Our results demonstrate that the sonic anemometer heating has a direct effect on temperature measurements while the turbulent wind field is not affected. As a consequence, fluxes of sensible heat are increased by an average 5 W m(-2) with activated heating, while no direct effect on other scalar fluxes was observed. However, the biased measurements in sensible heat fluxes can have an indirect effect on the CO2 fluxes in case they are used as input for a density-flux WPL correction of an open-path gas analyzer. Evaluating the self-heating effect of the open-path gas analyzer by comparing CO2 flux measurements between open- and closed-path gas analyzers, we found systematically higher CO2 uptake recorded with the open-path sensor, leading to a cumulative annual offset of 96 g Cm-2, which was not only the result of the cold winter season but also due to substantial self-heating effects during summer. With an inclined sensor mounting, only a fraction of the self-heating correction for vertically mounted instruments is required.
  • Köster, Kajar; Köster, Egle; Orumaa, Argo; Parro, Kristi; Jõgiste, Kalev; Berninger, Frank Alexander; Pumpanen, Jukka Sakari; Metslaid, Marek (2016)
    We compared the changes in aboveground biomass and initial recovery of C pools and CO2 efflux following fire disturbances in Scots pine (Pinus sylvesteris L.) stands with different time since stand-replacing fire. The study areas are located in hemiboreal vegetation zone, in north-western Estonia, in Vihterpalu. Six areas where the last fire occurred in the year 1837, 1940, 1951, 1982, 1997, and 2008 were chosen for the study. Our results show that forest fire has a substantial effect on the C content in the top soil layer, but not in the mineral soil layers. Soil respiration showed a chronological response to the time since the forest fire and the values were lowest in the area where the fire was in the year 2008. The respiration values also followed seasonal pattern being highest in August and lowest in May and November. The CO2 effluxes were lowest on the newly burned area through the entire growing season. There was also a positive correlation between soil temperature and soil respiration values in our study areas.
  • Viskari, Toni; Laine, Maisa; Kulmala, Liisa; Mäkelä, Jarmo; Fer, Istem; Liski, Jari (2020)
    Model-calculated forecasts of soil organic carbon (SOC) are important for approximating global terrestrial carbon pools and assessing their change. However, the lack of detailed observations limits the reliability and applicability of these SOC projections. Here, we studied whether state data assimilation (SDA) can be used to continuously update the modeled state with available total carbon measurements in order to improve future SOC estimations. We chose six fallow test sites with measurement time series spanning 30 to 80 years for this initial test. In all cases, SDA improved future projections but to varying degrees. Furthermore, already including the first few measurements impacted the state enough to reduce the error in decades-long projections by at least 1 tCha(-1). Our results show the benefits of implementing SDA methods for forecasting SOC as well as highlight implementation aspects that need consideration and further research.
  • Ribeiro-Kumara, Christine; Pumpanen, Jukka; Heinonsalo, Jussi; Metslaid, Marek; Orumaa, Argo; Jõgiste, Kalev; Berninger, Frank; Köster, Kajar (2020)
    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 179years 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 8years after fire, whereas soil moisture varied through the fire chronosequences without a consistent pattern. Litter decomposition and CO2 efflux were still lower 8years after fire compared with pre-fire levels (179years after fire). Both returned to pre-fire levels before vegetation re-established, and CO2 efflux was only strongly responsive to temperature from 19years 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.
  • Isakova, Elena P.; Matushkina, Irina N.; Popova, Tatyana N.; Dergacheva, Darya; Gessler, Natalya N.; Klein, Olga; Semenikhina, Anastasya; Deryabina, Yulia; La Porta, Nicola; Saris, Nils-Eric L. (2020)
    In this study, we evaluated the metabolic profile of the aerobic microorganism of Endomyces magnusii with a complete respiration chain and well-developed mitochondria system during long-lasting cultivation. The yeast was grown in batches using glycerol and glucose as the sole carbon source for a week. The profile included the cellular biological and chemical parameters, which determined the redox status of the yeast cells. We studied the activities of the antioxidant systems (catalases and superoxide dismutases), glutathione system enzymes (glutathione peroxidase and reductase), aconitase, as well as the main enzymes maintaining NADPH levels in the cells (glucose-6-phosphate dehydrogenase and NADP(+)-isocitrate dehydrogenase) during aging of Endomyces magnusii on two kinds of substrates. We also investigated the dynamics of change in oxidized and reduced glutathione, conjugated dienes, and reactive oxidative species in the cells at different growth stages, including the deep stationary stages. Our results revealed a similar trend in the changes in the activity of all the enzymes tested, which increased 2-4-fold upon aging. The yeast cytosol had a very high reduced glutathione content, 22 times than that of Saccharomyces cerevisiae, and remained unchanged during growth, whereas there was a 7.5-fold increase in the reduced glutathione-to-oxidized glutathione ratio. The much higher level of reactive oxidative species was observed in the cells in the late and deep stationary phases, especially in the cells using glycerol. Cell aging of the culture grown on glycerol, which promotes active oxidative phosphorylation in the mitochondria, facilitated the functioning of powerful antioxidant systems (catalases, superoxide dismutases, and glutathione system enzymes) induced by reactive oxidative species. Moreover, it stimulated NADPH synthesis, regulating the cytosolic reduced glutathione level, which in turn determines the redox potential of the yeast cell during the early aging process.
  • Graessler, Peter; Meyer, Nele; Peukert, Juergen; Welp, Gerhard; Damerow, Lutz; Lammers, Peter Schulze; Amelung, Wulf (2019)
    Hot vegetable oil can be used for weed control as an alternative to the use of herbicides. We analysed the temporal development of vegetable oil mineralization in soil and tested the role of nutrient supply on oil mineralization. Further, we investigated the effect of oil application on mineralization of native soil organic carbon (SOC), i.e. the priming effect. In a laboratory experiment, three oil dosages (0.1, 1.0 and 3.0ml per 35g soil) were applied to three arable soils and soil respiration was measured hourly. Both a C3-sunflower oil and a C4-corn oil were used in order to differentiate oil-derived CO2 from SOC-derived CO2. The results revealed that after 42days of incubation, 9.6 to 39.7% of the applied oil was mineralized which, however, also primed the mineralization of SOC by a factor of 2.2 to 4.2. The higher the applied oil amount, the lower was the percentage of oil-C mineralization, but the higher was the priming effect. The addition of fertilizer (0.29mgNg(-1) soil and 0.048mgPg(-1) soil) increased oil-C mineralization to 39.9 to 50.9%. We conclude that oil can temporarily accumulate in soil, especially in case of low nutrient supply. As the addition of oil stimulates SOC mineralization, a decrease of native SOC stocks may occur, which needs further quantification in long-term field experiments.
  • Chretien, Dominique; Benit, Paule; Ha, Hyung-Ho; Keipert, Susanne; El-Khoury, Riyad; Chang, Young-Tae; Jastroch, Martin; Jacobs, Howard T.; Rustin, Pierre; Rak, Malgorzata (2018)
    In endothermic species, heat released as a product of metabolism ensures stable internal temperature throughout the organism, despite varying environmental conditions. Mitochondria are major actors in this thermogenic process. Part of the energy released by the oxidation of respiratory substrates drives ATP synthesis and metabolite transport, but a substantial proportion is released as heat. Using a temperature-sensitive fluorescent probe targeted to mitochondria, we measured mitochondrial temperature in situ under different physiological conditions. At a constant external temperature of 38 degrees C, mitochondria were more than 10 degrees C warmer when the respiratory chain (RC) was fully functional, both in human embryonic kidney (HEK) 293 cells and primary skin fibroblasts. This differential was abolished in cells depleted of mitochondrial DNA or treated with respiratory inhibitors but preserved or enhanced by expressing thermogenic enzymes, such as the alternative oxidase or the uncoupling protein 1. The activity of various RC enzymes was maximal at or slightly above 50 degrees C. In view of their potential consequences, these observations need to be further validated and explored by independent methods. Our study prompts a critical re-examination of the literature on mitochondria.
  • Ignatenko, Olesia; Nikkanen, Joni; Kononov, Alexander; Zamboni, Nicola; Ince-Dunn, Gulayse; Suomalainen Wartiovaara, Anu (2020)
    Mitochondrial DNA (mtDNA) depletion syndrome (MDS) is a group of severe, tissue-specific diseases of childhood with unknown pathogenesis. Brain-specific MDS manifests as devastating spongiotic encephalopathy with no curative therapy. Here, we report cell type-specific stress responses and effects of rapamycin treatment and ketogenic diet (KD) in mice with spongiotic encephalopathy mimicking human MDS, as these interventions were reported to improve some mitochondrial disease signs or symptoms. Thesemice with astrocyte-specific knockout of Twnk gene encoding replicative mtDNA helicase Twinkle (TwKO(astro)) show wide-spread cell-autonomous astrocyte activation and mitochondrial integrated stress response (ISRmt) induction with major metabolic remodeling of the brain. Mice with neuronal-specific TwKO show no ISRmt. Both KD and rapamycin lead to rapid deterioration and weight loss of TwKO(astro) and premature trial termination. Although rapamycin had no robust effects on TwKO(astro) brain pathology, KD exacerbated spongiosis, gliosis, and ISRmt. Our evidence emphasizes that mitochondrial disease treatments and stress responses are tissue- and disease specific. Furthermore, rapamycin and KD are deleterious in MDS-linked spongiotic encephalopathy, pointing to a crucial role of diet and metabolism for mitochondrial disease progression.
  • Morioka, Hiroshi; Calhoun, Vince; Hyvarinen, Aapo (2020)
    Accumulating evidence from whole brain functional magnetic resonance imaging (fMRI) suggests that the human brain at rest is functionally organized in a spatially and temporally constrained manner. However, because of their complexity, the fundamental mechanisms underlying time-varying functional networks are still not well under-stood. Here, we develop a novel nonlinear feature extraction framework called local space-contrastive learning (LSCL), which extracts distinctive nonlinear temporal structure hidden in time series, by training a deep temporal convolutional neural network in an unsupervised, data-driven manner. We demonstrate that LSCL identifies certain distinctive local temporal structures, referred to as temporal primitives, which repeatedly appear at different time points and spatial locations, reflecting dynamic resting-state networks. We also show that these temporal primitives are also present in task-evoked spatiotemporal responses. We further show that the temporal primitives capture unique aspects of behavioral traits such as fluid intelligence and working memory. These re-sults highlight the importance of capturing transient spatiotemporal dynamics within fMRI data and suggest that such temporal primitives may capture fundamental information underlying both spontaneous and task-induced fMRI dynamics.
  • Kulmala, Liisa; Pumpanen, Jukka; Vesala, Timo; Hari, Pertti (2009)
    Heather (Calluna vulgaris), rosebay willowherb (Epilobium angustifolium), wavy hair-grass (Deschampsia flexuosa) and raspberry (Rubus idaeus) are typical species at boreal clear-cut sites. In this study, we measured their photosynthesis separately in the growing season of 2005 using a manual chamber. All measured species showed clear and species-specific seasonal cycles of photosynthetic activity (P-max). The maxima of C. vulgaris and E. angustifolium occurred around June and July, while that of R. idaeus occurred as late as August. A simple model of photosynthetic activity is presented, addressing the photosynthesis of C. vulgaris was mainly explained by temperature history when the soil moisture is high. The activity of deciduous D. flexuosa also followed the temperature history, unlike the activities of E. angustifolium and R. idaeus. During a short drought, some shoots decreased their P-max levels but none of the species showed similar reactions between individuals. We also observed that the comparison of the whole-plant P-max or respiration of different-sized individuals were less scattered than the results based on full-grown leaf mass, implying that species-specific rates of photosynthesis at ground level are rather similar regardless of the plant size. Using species composition and continuous temperature and light measurements, we upscaled the species-specific process rates and integrated fixed and respired CO2 of ground vegetation for the entire 2005 growing season. The photosynthetic production per surface area of soil was 760 g C m(-2) y(-1) at the fertile site and 300 g C m(-2) y(-1) at the infertile site. During the snow-free period (18 April-21 November), the above ground parts of measured species released 75 g C m(-2) y(-1) at the infertile site. At the fertile site, E. angustifolium and R. idaeus respired 22 and 12 g C m(-2) y(-1), respectively.
  • Koebsch, Franziska; Sonnentag, Oliver; Järveoja, Järvi; Peltoniemi, Mikko; Alekseychik, Pavel; Aurela, Mika; Arslan, Ali Nadir; Dinsmore, Kerry; Gianelle, Damiano; Helfter, Carole; Jackowicz-Korczynski, Marcin; Korrensalo, Aino; Leith, Fraser; Linkosalmi, Maiju; Lohila, Annalea; Lund, Magnus; Maddison, Martin; Mammarella, Ivan; Mander, Ülo; Minkkinen, Kari; Pickard, Amy; Pullens, Johannes W.M.; Tuittila, Eeva-Stiina; Nilsson, Mats B.; Peichl, Matthias (2020)
    Abstract The role of plant phenology as regulator for gross ecosystem productivity (GEP) in peatlands is empirically not well constrained. This is because proxies to track vegetation development with daily coverage at the ecosystem scale have only recently become available and the lack of such data has hampered the disentangling of biotic and abiotic effects. This study aimed at unraveling the mechanisms that regulate the seasonal variation in GEP across a network of eight European peatlands. Therefore, we described phenology with canopy greenness derived from digital repeat photography and disentangled the effects of radiation, temperature and phenology on GEP with commonality analysis and structural equation modeling. The resulting relational network could not only delineate direct effects but also accounted for possible effect combinations such as interdependencies (mediation) and interactions (moderation). We found that peatland GEP was controlled by the same mechanisms across all sites: phenology constituted a key predictor for the seasonal variation in GEP and further acted as distinct mediator for temperature and radiation effects on GEP. In particular, the effect of air temperature on GEP was fully mediated through phenology, implying that direct temperature effects representing the thermoregulation of photosynthesis were negligible. The tight coupling between temperature, phenology and GEP applied especially to high latitude and high altitude peatlands and during phenological transition phases. Our study highlights the importance of phenological effects when evaluating the future response of peatland GEP to climate change. Climate change will affect peatland GEP especially through changing temperature patterns during plant-phenologically sensitive phases in high latitude and high altitude regions.
  • Denfeld, Blaize A.; Kortelainen, Pirkko; Rantakari, Miitta; Sobek, Sebastian; Weyhenmeyer, Gesa A. (2016)
    Northern lakes are ice-covered for considerable portions of the year, where carbon dioxide (CO2) can accumulate below ice, subsequently leading to high CO2 emissions at ice-melt. Current knowledge on the regional control and variability of below ice partial pressure of carbon dioxide (pCO(2)) is lacking, creating a gap in our understanding of how ice cover dynamics affect the CO2 accumulation below ice and therefore CO2 emissions from inland waters during the ice-melt period. To narrow this gap, we identified the drivers of below ice pCO(2) variation across 506 Swedish and Finnish lakes using water chemistry, lake morphometry, catchment characteristics, lake position, and climate variables. We found that lake depth and trophic status were the most important variables explaining variations in below ice pCO(2) across the 506 lakes(.) Together, lake morphometry and water chemistry explained 53% of the site-to-site variation in below ice pCO(2). Regional climate (including ice cover duration) and latitude only explained 7% of the variation in below ice pCO(2). Thus, our results suggest that on a regional scale a shortening of the ice cover period on lakes may not directly affect the accumulation of CO2 below ice but rather indirectly through increased mobility of nutrients and carbon loading to lakes. Thus, given that climate-induced changes are most evident in northern ecosystems, adequately predicting the consequences of a changing climate on future CO2 emission estimates from northern lakes involves monitoring changes not only to ice cover but also to changes in the trophic status of lakes.