In situ short-term responses of Amazonian understory plants to elevated CO2

The response of plants to increasing atmospheric CO2 depends on the ecological context where the plants are found. Several experiments with elevated CO2 (eCO2) have been done worldwide, but the Amazonian forest understory has been neglected. As the central Amazon is limited by light and phosphorus, understanding how understory responds to eCO2 is important for foreseeing how the forest will function in the future. In the understory of a natural forest in the Central Amazon, we installed four open-top chambers as control replicates and another four under eCO2 (+250 ppm above ambient levels). Under eCO2, we observed increases in carbon assimilation rate (67%), maximum electron transport rate (19%), quantum yield (56%), and water use efficiency (78%). We also detected an increase in leaf area (51%) and stem diameter increment (65%). Central Amazon understory responded positively to eCO2 by increasing their ability to capture and use light and the extra primary productivity was allocated to supporting more leaf and conducting tissues. The increment in leaf area while maintaining transpiration rates suggests that the understory will increase its contribution to evapotranspiration. Therefore, this forest might be less resistant in the future to extreme drought, as no reduction in transpiration rates were detected.

Drainage effects on carbon budgets of degraded peatlands in the north of the Netherlands

Peatlands store vast amounts of carbon (C). However, land-use-driven drainage causes peat oxidation, resulting in CO2 emission. There is a growing need for ground-truthing CO2 emission and its potential drivers to better quantify long-term emission trends in peatlands. This will help improve National Inventory Reporting and ultimately aid the design and verification of mitigation measures. To investigate regional drivers of CO2 emission, we estimated C budgets using custom-made automated chamber systems measuring CO2 concentrations corrected for carbon export and import. Chamber systems were rotated among thirteen degraded peatland pastures in Friesland (the Netherlands). These peatlands varied in water table depth (WTD), drainage-irrigation management (fixed regulated ditch water level (DWL), subsurface irrigation, furrow irrigation, or dynamic regulated DWL), and soil moisture. We investigated (1) whether drainage-irrigation management and related hydrological drivers could explain variation in C budgets, (2) how nighttime ecosystem respiration (Reconight) related to hydrological drivers, and (3) how C budgets compared with estimates from Tier 1 and Tier 2 models regularly used in National Inventory Reporting. Deep-drained peatlands largely overlapped with C budgets from shallow-drained peatlands. The variation in C budgets could not be explained with drainage-irrigation measures or annual WTD, likely because of high variation between sites. Reconightincreased from 85 to 250 kg CO2 ha-1 day-1 as the WTD dropped from 0 to 50 cm across all sites. A deeper WTD had no apparent effect on Reconight, which could be explained by the unimodal relationship we found between Reconight and soil moisture. Finally, C budgets estimated by Tier 1 emission factors and Tier 2 national models mismatched the between-site and between-year variation found in chamber-based estimated NECBs. To conclude, our study showed that shallow WTDs greatly determine C budgets and that regional C budgets, which can be accurately measure with periodic automated chamber measurements, are instrumental for model validation.

Diel and seasonal stem growth responses to climatic variation are consistent across species in a subtropical tree community

Understanding how intra-annual stem growth responds to atmospheric and soil conditions is essential for assessing the effects of climate extremes on forest productivity. In species-poor forests, such understanding can be obtained by studying stem growth of the dominant species. Yet, in species-rich (sub-)tropical forests, it is unclear whether these responses are consistent among species. We monitored intra-annual stem growth with high-resolution dendrometers for 27 trees belonging to 14 species over 5 yr in a montane subtropical forest. We quantified diel and seasonal stem growth patterns, verified to what extent observed growth patterns coincide across species and analysed their main climatic drivers. We found very consistent intra-annual growth patterns across species. Species varied in the rate but little in the timing of growth. Diel growth patterns revealed that - across species - trees mainly grew before dawn when vapour pressure deficit (VPD) was low. Within the year, trees mainly grew between May and August driven by temperature and VPD, but not by soil moisture. Our study reveals highly consistent stem growth patterns and climatic drivers at community level. Further studies are needed to verify whether these results hold across climates and forests, and whether they can be scaled up to estimate forest productivity.

Monitoring of carbon-water fluxes at Eurasian meteorological stations using random forest and remote sensing

Simulating the carbon-water fluxes at more widely distributed meteorological stations based on the sparsely and unevenly distributed eddy covariance flux stations is needed to accurately understand the carbon-water cycle of terrestrial ecosystems. We established a new framework consisting of machine learning, determination coefficient (R2), Euclidean distance, and remote sensing (RS), to simulate the daily net ecosystem carbon dioxide exchange (NEE) and water flux (WF) of the Eurasian meteorological stations using a random forest model or/and RS. The daily NEE and WF datasets with RS-based information (NEE-RS and WF-RS) for 3774 and 4427 meteorological stations during 2002-2020 were produced, respectively. And the daily NEE and WF datasets without RS-based information (NEE-WRS and WF-WRS) for 4667 and 6763 meteorological stations during 1983-2018 were generated, respectively. For each meteorological station, the carbon-water fluxes meet accuracy requirements and have quasi-observational properties. These four carbon-water flux datasets have great potential to improve the assessments of the ecosystem carbon-water dynamics.

ForestClim-Bioclimatic variables for microclimate temperatures of European forests

Microclimate research gained renewed interest over the last decade and its importance for many ecological processes is increasingly being recognized. Consequently, the call for high-resolution microclimatic temperature grids across broad spatial extents is becoming more pressing to improve ecological models. Here, we provide a new set of open-access bioclimatic variables for microclimate temperatures of European forests at 25 × 25 m² resolution.

Drought resilience of conifer species is driven by leaf lifespan but not by hydraulic traits

Increased droughts impair tree growth worldwide. This study analyzes hydraulic and carbon traits of conifer species, and how they shape species strategies in terms of their growth rate and drought resilience. We measured 43 functional stem and leaf traits for 28 conifer species growing in a 50-yr-old common garden experiment in the Netherlands. We assessed: how drought- and carbon-related traits are associated across species, how these traits affect stem growth and drought resilience, and how traits and drought resilience are related to species' climatic origin. We found two trait spectra: a hydraulics spectrum reflecting a trade-off between hydraulic and biomechanical safety vs hydraulic efficiency, and a leaf economics spectrum reflecting a trade-off between tough, long-lived tissues vs high carbon assimilation rate. Pit aperture size occupied a central position in the trait-based network analysis and also increased stem growth. Drought recovery decreased with leaf lifespan. Conifer species with long-lived leaves suffer from drought legacy effects, as drought-damaged leaves cannot easily be replaced, limiting growth recovery after drought. Leaf lifespan, rather than hydraulic traits, can explain growth responses to a drier future.

Changes in leaf functional traits with leaf age: when do leaves decrease their photosynthetic capacity in Amazonian trees?

Most leaf functional trait studies in the Amazon basin do not consider ontogenetic variations (leaf age), which may influence ecosystem productivity throughout the year. When leaf age is taken into account, it is generally considered discontinuous, and leaves are classified into age categories based on qualitative observations. Here, we quantified age-dependent changes in leaf functional traits such as the maximum carboxylation rate of ribulose-1,5-biphosphate carboxylase/oxygenase (Rubisco) (Vcmax), stomatal control (Cgs%), leaf dry mass per area and leaf macronutrient concentrations for nine naturally growing Amazon tropical trees with variable phenological strategies. Leaf ages were assessed by monthly censuses of branch-level leaf demography; we also performed leaf trait measurements accounting for leaf chronological age based on days elapsed since the first inclusion in the leaf demography, not predetermined age classes. At the tree community scale, a nonlinear relationship between Vcmax and leaf age existed: young, developing leaves showed the lowest mean photosynthetic capacity, increasing to a maximum at 45 days and then decreasing gradually with age in both continuous and categorical age group analyses. Maturation times among species and phenological habits differed substantially, from 8 ± 30 to 238 ± 30 days, and the rate of decline of Vcmax varied from -0.003 to -0.065 μmol CO2 m-2 s-1 day-1. Stomatal control increased significantly in young leaves but remained constant after peaking. Mass-based phosphorus and potassium concentrations displayed negative relationships with leaf age, whereas nitrogen did not vary temporally. Differences in life strategies, leaf nutrient concentrations and phenological types, not the leaf age effect alone, may thus be important factors for understanding observed photosynthesis seasonality in Amazonian forests. Furthermore, assigning leaf age categories in diverse tree communities may not be the recommended method for studying carbon uptake seasonality in the Amazon, since the relationship between Vcmax and leaf age could not be confirmed for all trees.

ForestTemp - Sub-canopy microclimate temperatures of European forests

Ecological research heavily relies on coarse-gridded climate data based on standardized temperature measurements recorded at 2 m height in open landscapes. However, many organisms experience environmental conditions that differ substantially from those captured by these macroclimatic (i.e. free air) temperature grids. In forests, the tree canopy functions as a thermal insulator and buffers sub-canopy microclimatic conditions, thereby affecting biological and ecological processes. To improve the assessment of climatic conditions and climate-change-related impacts on forest-floor biodiversity and functioning, high-resolution temperature grids reflecting forest microclimates are thus urgently needed. Combining more than 1200 time series of in situ near-surface forest temperature with topographical, biological and macroclimatic variables in a machine learning model, we predicted the mean monthly offset between sub-canopy temperature at 15 cm above the surface and free-air temperature over the period 2000-2020 at a spatial resolution of 25 m across Europe. This offset was used to evaluate the difference between microclimate and macroclimate across space and seasons and finally enabled us to calculate mean annual and monthly temperatures for European forest understories. We found that sub-canopy air temperatures differ substantially from free-air temperatures, being on average 2.1°C (standard deviation ± 1.6°C) lower in summer and 2.0°C higher (±0.7°C) in winter across Europe. Additionally, our high-resolution maps expose considerable microclimatic variation within landscapes, not captured by the gridded macroclimatic products. The provided forest sub-canopy temperature maps will enable future research to model below-canopy biological processes and patterns, as well as species distributions more accurately.

Altered energy partitioning across terrestrial ecosystems in the European drought year 2018

Drought and heat events, such as the 2018 European drought, interact with the exchange of energy between the land surface and the atmosphere, potentially affecting albedo, sensible and latent heat fluxes, as well as CO₂ exchange. Each of these quantities may aggravate or mitigate the drought, heat, their side effects on productivity, water scarcity and global warming. We used measurements of 56 eddy covariance sites across Europe to examine the response of fluxes to extreme drought prevailing most of the year 2018 and how the response differed across various ecosystem types (forests, grasslands, croplands and peatlands). Each component of the surface radiation and energy balance observed in 2018 was compared to available data per site during a reference period 2004-2017. Based on anomalies in precipitation and reference evapotranspiration, we classified 46 sites as drought affected. These received on average 9% more solar radiation and released 32% more sensible heat to the atmosphere compared to the mean of the reference period. In general, drought decreased net CO₂ uptake by 17.8%, but did not significantly change net evapotranspiration. The response of these fluxes differed characteristically between ecosystems; in particular, the general increase in the evaporative index was strongest in peatlands and weakest in croplands. This article is part of the theme issue 'Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale'.

The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data

The FLUXNET2015 dataset provides ecosystem-scale data on CO₂, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.

Measurement(s)	net ecosystem exchange • carbon dioxide • water • energy
Technology Type(s)	eddy covariance • measurement device
Sample Characteristic - Environment	terrestrial biome • atmosphere
Sample Characteristic - Location	Earth (planet)

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12295910

Flood tolerance in two tree species that inhabit both the Amazonian floodplain and the dry Cerrado savanna of Brazil

Comparing plants of the same species thriving in flooded and non-flooded ecosystems helps to clarify the interplay between natural selection, phenotypic plasticity and stress adaptation. We focussed on responses of seeds and seedlings of Genipa americana and Guazuma ulmifolia to substrate waterlogging or total submergence. Both species are commonly found in floodplain forests of Central Amazonia and in seasonally dry savannas of Central Brazil (Cerrado). Although seeds of Amazonian and Cerrado G. americana were similar in size, the germination percentage of Cerrado seeds was decreased by submergence (3 cm water) and increased in Amazonian seeds. The seeds of Amazonian G. ulmifolia were heavier than Cerrado seeds, but germination of both types was unaffected by submergence. Three-month-old Amazonian and Cerrado seedlings of both species survived 30 days of waterlogging or submersion despite suffering significant inhibition in biomass especially if submerged. Shoot elongation was also arrested. Submersion triggered chlorosis and leaf abscission in Amazonian and Cerrado G. ulmifolia while waterlogging did so only in Cerrado seedlings. During 30 days of re-exposure to non-flooded conditions, G. ulmifolia plants that lost their leaves produced a replacement flush. However, they attained only half the plant dry mass of non-flooded plants. Both submerged and waterlogged G. americana retained their leaves. Consequently, plant dry mass after 30 days recovery was less depressed by these stresses than in G. ulmifolia. Small amounts of cortical aerenchyma were found in roots 2 cm from the tip of well-drained plants. The amount was increased by flooding. Waterlogging but not submergence promoted hypertrophy of lenticels at the stem base of both species and adventitious rooting in G. ulmifolia. Despite some loss of performance in dryland plants, flood tolerance traits were present in wetland and dryland populations of both species. They are part of an overall stress-response potential that permits flexible acclimation to locally flooded conditions.

Widespread reduction in sun-induced fluorescence from the Amazon during the 2015/2016 El Niño

The tropical carbon balance dominates year-to-year variations in the CO₂ exchange with the atmosphere through photosynthesis, respiration and fires. Because of its high correlation with gross primary productivity (GPP), observations of sun-induced fluorescence (SIF) are of great interest. We developed a new remotely sensed SIF product with improved signal-to-noise in the tropics, and use it here to quantify the impact of the 2015/2016 El Niño Amazon drought. We find that SIF was strongly suppressed over areas with anomalously high temperatures and decreased levels of water in the soil. SIF went below its climatological range starting from the end of the 2015 dry season (October) and returned to normal levels by February 2016 when atmospheric conditions returned to normal, but well before the end of anomalously low precipitation that persisted through June 2016. Impacts were not uniform across the Amazon basin, with the eastern part experiencing much larger (10-15%) SIF reductions than the western part of the basin (2-5%). We estimate the integrated loss of GPP relative to eight previous years to be 0.34-0.48 PgC in the three-month period October-November-December 2015.This article is part of a discussion meeting issue 'The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications'.

Data for developing allometric models and evaluating carbon stocks of the Zambezi Teak Forests in Zambia

This paper presents data on carbon stocks of tropical tree species along a rainfall gradient. The data was generated from the Sesheke, Namwala, and Kabompo sites in Zambia. Though above-ground data was generated for all these three sites, we uprooted trees to determine below-ground biomass from the Sesheke site only. The vegetation was assessed in all three sites. The data includes tree diameter at breast height (DBH), total tree height, wood density, wood dry weight and root dry weight for large (≥ 5 cm DBH) and small (< 5 cm DBH) trees. We further presented Root-to-Shoot Ratios of uprooted trees. Data on the importance-value indices of various species for large and small trees are also determined. Below and above-ground carbon stocks of the surveyed tree species are presented per site. This data were used by Ngoma et al. (2018) [1] to develop above and below-ground biomass models and the reader is referred to this study for additional information, interpretation, and reflection on applying this data.

Variation in stem mortality rates determines patterns of above-ground biomass in Amazonian forests: implications for dynamic global vegetation models

Understanding the processes that determine above-ground biomass (AGB) in Amazonian forests is important for predicting the sensitivity of these ecosystems to environmental change and for designing and evaluating dynamic global vegetation models (DGVMs). AGB is determined by inputs from woody productivity [woody net primary productivity (NPP)] and the rate at which carbon is lost through tree mortality. Here, we test whether two direct metrics of tree mortality (the absolute rate of woody biomass loss and the rate of stem mortality) and/or woody NPP, control variation in AGB among 167 plots in intact forest across Amazonia. We then compare these relationships and the observed variation in AGB and woody NPP with the predictions of four DGVMs. The observations show that stem mortality rates, rather than absolute rates of woody biomass loss, are the most important predictor of AGB, which is consistent with the importance of stand size structure for determining spatial variation in AGB. The relationship between stem mortality rates and AGB varies among different regions of Amazonia, indicating that variation in wood density and height/diameter relationships also influences AGB. In contrast to previous findings, we find that woody NPP is not correlated with stem mortality rates and is weakly positively correlated with AGB. Across the four models, basin-wide average AGB is similar to the mean of the observations. However, the models consistently overestimate woody NPP and poorly represent the spatial patterns of both AGB and woody NPP estimated using plot data. In marked contrast to the observations, DGVMs typically show strong positive relationships between woody NPP and AGB. Resolving these differences will require incorporating forest size structure, mechanistic models of stem mortality and variation in functional composition in DGVMs.

Variation in stem mortality rates determines patterns of above-ground biomass in Amazonian forests: implications for dynamic global vegetation models

Understanding the processes that determine above-ground biomass (AGB) in Amazonian forests is important for predicting the sensitivity of these ecosystems to environmental change and for designing and evaluating dynamic global vegetation models (DGVMs). AGB is determined by inputs from woody productivity [woody net primary productivity (NPP)] and the rate at which carbon is lost through tree mortality. Here, we test whether two direct metrics of tree mortality (the absolute rate of woody biomass loss and the rate of stem mortality) and/or woody NPP, control variation in AGB among 167 plots in intact forest across Amazonia. We then compare these relationships and the observed variation in AGB and woody NPP with the predictions of four DGVMs. The observations show that stem mortality rates, rather than absolute rates of woody biomass loss, are the most important predictor of AGB, which is consistent with the importance of stand size structure for determining spatial variation in AGB. The relationship between stem mortality rates and AGB varies among different regions of Amazonia, indicating that variation in wood density and height/diameter relationships also influences AGB. In contrast to previous findings, we find that woody NPP is not correlated with stem mortality rates and is weakly positively correlated with AGB. Across the four models, basin-wide average AGB is similar to the mean of the observations. However, the models consistently overestimate woody NPP and poorly represent the spatial patterns of both AGB and woody NPP estimated using plot data. In marked contrast to the observations, DGVMs typically show strong positive relationships between woody NPP and AGB. Resolving these differences will require incorporating forest size structure, mechanistic models of stem mortality and variation in functional composition in DGVMs.

After more than a decade of soil moisture deficit, tropical rainforest trees maintain photosynthetic capacity, despite increased leaf respiration

Determining climate change feedbacks from tropical rainforests requires an understanding of how carbon gain through photosynthesis and loss through respiration will be altered. One of the key changes that tropical rainforests may experience under future climate change scenarios is reduced soil moisture availability. In this study we examine if and how both leaf photosynthesis and leaf dark respiration acclimate following more than 12 years of experimental soil moisture deficit, via a through-fall exclusion experiment (TFE) in an eastern Amazonian rainforest. We find that experimentally drought-stressed trees and taxa maintain the same maximum leaf photosynthetic capacity as trees in corresponding control forest, independent of their susceptibility to drought-induced mortality. We hypothesize that photosynthetic capacity is maintained across all treatments and taxa to take advantage of short-lived periods of high moisture availability, when stomatal conductance (gs ) and photosynthesis can increase rapidly, potentially compensating for reduced assimilate supply at other times. Average leaf dark respiration (Rd ) was elevated in the TFE-treated forest trees relative to the control by 28.2 ± 2.8% (mean ± one standard error). This mean Rd value was dominated by a 48.5 ± 3.6% increase in the Rd of drought-sensitive taxa, and likely reflects the need for additional metabolic support required for stress-related repair, and hydraulic or osmotic maintenance processes. Following soil moisture deficit that is maintained for several years, our data suggest that changes in respiration drive greater shifts in the canopy carbon balance, than changes in photosynthetic capacity.

Nocturnal accumulation of CO2 underneath a tropical forest canopy along a topographical gradient

Flux measurements of carbon dioxide and water vapor above tropical rain forests are often difficult to interpret because the terrain is usually complex. This complexity induces heterogeneity in the surface but also affects lateral movement of carbon dioxide (CO2) not readily detected by the eddy covariance systems. This study describes such variability using measurements of CO2 along vertical profiles and along a toposequence in a tropical rain forest near Manaus, Brazil. Seasonal and diurnal variation was recorded, with atmospheric CO2 concentration maxima around dawn, generally higher CO2 build-up in the dry season and stronger daytime CO2 drawdown in the wet season. This variation was reflected all along the toposequence, but the slope and valley bottom accumulated clearly more CO2 than the plateaus, depending on atmospheric stability. Particularly during stable nights, accumulation was along lines of equal altitude, suggesting that large amounts of CO2 are stored in the valleys of the landscape. Flushing of this store only occurs during mid-morning, when stored CO2 may well be partly transported back to the plateaus. It is clear that, for proper interpretation of tower fluxes in such complex and actively respiring terrain, the horizontal variability of storage needs to be taken into account not only during the night but also during the mornings.

Laser speckle imaging of dynamic changes in flow during photodynamic therapy

We present a study investigating the use of laser speckle imaging (LSI) for monitoring blood flow during photodynamic therapy (PDT) utilizing the therapeutic illumination radiation. The coherent nature of a laser source, often used in PDT, offers the possibility of obtaining information on the blood flow without interrupting treatment. We have found that in the rat skin-fold observation chamber, it is possible to monitor the vasculature response to PDT in individual arteries, veins and in tumour microvasculature with significantly higher spatial and temporal resolution than current methods. This illustrates the potential for LSI for monitoring PDT, in particular for vascular-localizing photosensitizers, where current non-invasive methods are difficult because of high absorption due to blood and the specific localization of photosensitizer within the vasculature. However, critical problems need to be further investigated and solved, like the influence of tissue sampling volume, changing of optical properties and movement artefacts from other vessels on the LSI signal. Until then, the real potential of LSI for monitoring blood flow remains of limited value.

Phosphorescence-Fluorescence ratio imaging for monitoring the oxygen status during photodynamic therapy

The effectiveness of photodynamic therapy is strongly dependent on the availabilty of oxygen. In the present paper we show that the ratio between photosensitiser phosphorescence and fluorescence is a parameter that can be used to monitor the competition between singlet oxygen production and other processes quenching the photosensitiser triplet state. We present a theoretical basis for the validity of this approach and a series of in vitro imaging experiments.

Photosynthetic capacity in a central Amazonian rain forest

The vertical profile in leaf photosynthetic capacity was investigated in a terra firme rain forest in central Amazonia. Measurements of photosynthesis were made on leaves at five levels in the canopy, and a model was fitted to describe photosynthetic capacity for each level. In addition, vertical profiles of photosynthetic photon flux density, leaf nitrogen concentration and specific leaf area were measured. The derived parameters for maximum rate of electron transport (J(max)) and maximum rate of carboxylation by Rubisco (V(cmax)) increased significantly with canopy height (P < 0.05). The highest J(max) for a single canopy level was measured at the penultimate canopy level (20 m) and was 103.9 &mgr;mol m(-2) s(-1) +/- 24.2 (SE). The highest V(cmax) per canopy height was recorded at the top canopy level (24 m) and was 42.8 +/- 5.9 &mgr;mol m(-2) s(-1). Values of J(max) and V(cmax) at ground level were 35.8 +/- 3.3 and 20.5 +/- 1.3 &mgr;mol m(-2) s(-1), espectively. The increase in photosynthetic capacity with increasing canopy height was strongly correlated with leaf nitrogen concentration when examined on a leaf area basis, but was only weakly correlated on a mass basis. The correlation on an area basis can be largely explained by the concomitant decrease in specific leaf area with increasing height. Apparent daytime leaf respiration, on an area basis, also increased significantly with canopy height (P < 0.05). We conclude that canopy photosynthetic capacity can be represented as an average vertical profile, perturbations of which may be explained by variations in the environmental variables driving photosynthesis.