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Arctic terrestrial ecosystems near the treeline in river lowlands are vulnerable to the changing climate and seasonal extreme events, including flooding. We set up a simple camera monitoring system to record the timings and durations of the leafy period and the spring flush of river water at three observation sites (Boydom [B]: 70.64°N, 148.15°E; Kodac [K]:70.56°N, 148.26°E; Verkhny‐Khatistakh [VK]:70.25°N,147.47°E) in the Indigirka lowland, in Northeastern Siberia. Time‐lapse digital cameras were located at seven points across the three sites. The time intervals were 1–4 or 24 hours. The minimum and maximum monitoring periods were 2 years (July 2016 to August 2018) at B and 5 years (August 2013 to July 2018) at K. One camera documented the timings of river ice melt and open water periods from the riverbank of the Kryvaya River, one of the small tributaries of the Indigirka River. The other six cameras recorded several types of ground cover typical of the area, including larch trees (Larix cajanderi), shrubs (including Salix spp. and Betula nana), forbs, mosses and graminoids in an ecosystem of sparsely forested shrublands, wetlands and riversides. The data consists of 45,617 JPEG‐format images. This dataset can be used to detect the onset and offset of the growing season and to capture the ice melt timing and water cover periods in wetlands and riversides. It may be useful in validating satellite data such as the vegetation remote sensing index for remote and little‐known areas. These data may contribute to the study of the role of high‐latitude ecosystems in global climate changes. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2020-02.1/jalter-en. [Correction added on 7 September 2020, after first online publication: JaLTER URL has been updated.] [ABSTRACT FROM AUTHOR]

• Row orientations with smaller row–sun angles reduce solar-induced fluorescence. • Observed canopy SIF validated a 3D crop-row SIF radiative transfer model. • Simulated fluorescence escape ratio varied widely due to geometry and structures. • The inter-row widths affected simulated SIF under smaller row–sun angles. Although multiple studies have used solar-induced chlorophyll fluorescence (SIF) of the crop canopy to estimate photosynthetic activity, the effect of canopy geometry (row orientation) on diurnal SIF remains uncertain. Using a combination of 3D canopy radiative transfer modeling and spectroscopic observations collected in a winter wheat field, we investigated (i) the relationships between observed SIF and factors including temperature, humidity, absorbed photosynthetically active radiation (APAR), and row orientation; (ii) the temporal pattern and multi-angle distribution of diurnal canopy SIF; and (iii) the mechanisms influencing components of diurnal SIF under the effect of row orientation. The relationship between observed SIF and APAR was relatively strong at the early growth period, but SIF was influenced by various factors (temperature, humidity, and row–sun angle) at the middle of the growth period. To test an asymmetric crop row effect as a potential cause of this skewness, we evaluated the modeled SIF with a 3D northwestward (315°) crop row alignment and other orientations. Each row orientation resulted in a trough-like depression parallel to the row in simulated canopy SIF, which could cause a diurnal asymmetry of canopy SIF, a fraction of fluorescence escape, and a fraction of APAR. View angles, the dimension of canopy objects (1D/3D), inter-row width, and leaf structure parameters impacted the representativeness of these simulations. An increased shade SIF, synchronized with the time when row–sun angles become zero at the incident sunlight being parallel to the crop row, was linked to decreasing canopy SIF emissions and would cause a non-linear SIF–APAR relationship at certain row orientations especially facing diagonally to the south. The concept of row orientation provides a novel viewpoint of diurnal canopy SIF from which to test the effect of row geometry in cropland, and will promote a mechanistic understanding of photosynthesis and canopy light use. [ABSTRACT FROM AUTHOR]

Solar-induced chlorophyll fluorescence (SIF) can represent gross primary productivity (GPP) in many types of terrestrial vegetation. In principle, the chlorophyll- a fluorescence signal responds to the amount of light absorption and the fraction of energy distribution in photosystems. Therefore, it is mechanistically linked with CO 2 assimilation. Recently, radiative transfer models have traced the processes of emission, interception and reabsorption within a canopy in heterogeneous tree stands. These processes influence the expected relationship between SIF and GPP. We inferred that the vertical profile of SIF could reveal those processes. In addition, the sum of SIF emission from different pathways within the canopy must be equivalent to the total SIF emission from all leaves. The purposes of this study were: (1) to clarify the seasonal and diurnal variations of ground-based SIF observed above the overstory, midstory and understory layers (strata); (2) to examine whether the sum of SIF observed from the three layers could represent total SIF emissions, and (3) to examine whether SIF above the understory could reveal the photosynthetic activity within the vertical profile of a forest. To estimate how much SIF was present after its emission from leaves within the canopy, we conducted spectral radiation observations in three vertical layers: above the understory, midstory and overstory (8, 14 and 18 m from the ground, respectively) to retrieve the red and far-red SIF in a deciduous broadleaf forest ecosystem in Japan from April to November 2020. We found that SIF above the overstory and the sum of SIF from the three layers increased sharply at the leaf-onset of the overstory and was correlated with each season's GPP. The sum of far-red SIF from the three layers was proportional to the total SIF estimated using the escape ratio approach for SIF above the overstory. In this study we demonstrated that SIF above the understory could detect the increased photosynthesis of the understory in spring, compared with the GPP and the vertical profile of the CO 2 concentrations. In summary, SIF observed in three forest layers detected the seasonal change of GPP within the canopy. Thus, a multi-layer approach can be used to understand the relationship between SIF and photosynthesis within the canopy. • We identified solar-induced chlorophyll fluorescence (SIF) from 3 forest layers. • The SIF from different forest layers can detect seasonal photosynthetic activity. • The sum of overstory, midstory, and understory SIF could verify total SIF emissions. • Understory SIF responded to photosynthesis before leaf-onset in the overstory. [ABSTRACT FROM AUTHOR]

Solar-induced chlorophyll fluorescence (SIF) emissions were estimated by the "area-ratio Fraunhofer line depth (aFLD) method", a new retrieval methodology in spectra from a low spectral resolution (SR) spectroradiometer (MS-700: full width half maximum (FWHM) of 10 nm and spectral sampling interval of 3.3 nm), assisted with a scaling to reference SIF detected from high SR spectrum. The sparse pixels of a spectrum of low SR misses detecting the minimum of the O2A absorption band around at 760 nm, which makes the SIF detection by conventional FLD methods lose accuracy considerably. To overcome this, the aFLD method uses the definite integral of spectra over a wide interval between 750 and 780 nm. The integration of the spectrum is insusceptible to the change in shape of the depression curve, leading to higher accuracy of the aFLD method. Daily SIF, calculated by the aFLD method using the spectra obtained with MS-700, was scaled to reference daily SIF calculated by the spectral fitting method using the spectra obtained from August to December 2019 with an ultrafine SR spectroradiometer (QE Pro, FWHM = 0.24 nm). As a result, SIF calculated from MS-700 spectra by aFLD method was strongly correlated with the reference SIF from QE Pro spectra (r2 = 0.81) and was successfully scaled. Then, the scaled 11-year SIF from MS-700 at a deciduous broadleaf forest showed the correlation with GPP at multiple time steps: daily, monthly, and yearly, consistently during 2008–2018. The comparison of aFLD-derived SIF with the global Orbiting Carbon Observatory-2 (OCO-2) SIF data set (GOSIF) showed high correlation on monthly values during 2008–2017 (r2 = 0.85). The combining approach of the aFLD method with a scaling to reference SIF successfully detected long-term canopy SIF emissions, which has great potential to provide essential information on ecosystem-level photosynthesis. [ABSTRACT FROM AUTHOR]

• SIF red and SIF far-red were measured during the mid to late stage of a rice paddy growing season. • Similar to SIF far-red , SIF red showed a strong correlation to eddy GPP. • Canopy-escaping SIF far-red displayed a higher correlation with GPP than Total SIF far-red. • SIF is mainly controlled by physiology in relatively mature rice ecosystems. Terrestrial ecosystem photosynthesis plays a crucial role in global carbon cycling. Solar-induced chlorophyll fluorescence (SIF) is a state-of-the-art proxy for ecosystem photosynthesis. Although satellite-derived SIF correlates with gross primary productivity (GPP), it needs to be complemented with ground-based measurements to better understand the dynamics of carbon uptake by plants, because of the coarse spatiotemporal resolution of satellite-based data. We used an ultrafine-resolution spectrometer to detect both red SIF (SIF red , 687 nm) and far-red SIF (SIF far-red , 760 nm) at ground level. Then, we investigated how well they represented eddy-tower-derived GPP in a rice field of central Japan during the mid to late growing season in 2019. Half-hourly and daily averaged SIF red showed stronger correlation with GPP (R 2 = 0.61 and 0.83, respectively) than SIF far-red (R 2 = 0.42 and 0.57, respectively). Stronger seasonal correlation with GPP was observed for canopy-escaping SIF than for total SIF. The SIF red /SIF far-red ratio was not significantly correlated with seasonal changes in the normalized difference vegetation index or in the pigment-specific simple ratios for chlorophyll- a and - b. There were no clear differences in the SIF red –GPP relationships between sunny and cloudy conditions. We concluded that SIF red could be an equivalent or better proxy than SIF far-red for ecosystem-level photosynthesis. We further postulated that SIF emission is mainly controlled by plant physiology during the mid to late growing season, when temporal variations of the canopy structure in rice ecosystems are small. [ABSTRACT FROM AUTHOR]

The warming trend in the Arctic region is expected to cause drastic changes including permafrost degradation and vegetation shifts. We investigated the spatial distribution of ice content and stable isotopic compositions of water in near-surface permafrost down to a depth of 1 m in the Indigirka River lowlands of northeastern Siberia to examine how the permafrost conditions control vegetation and microtopography in the Taiga–Tundra boundary ecosystem. The gravimetric water content (GWC) in the frozen soil layer was significantly higher at microtopographically high elevations with growing larch trees (i.e., tree mounds) than at low elevations with wetland vegetation (i.e., wet areas). The observed ground ice (ice-rich layer) with a high GWC in the tree mounds suggests that the relatively elevated microtopography of the land surface, which was formed by frost heave, strongly affects the survival of larch trees. The isotopic composition of the ground ice indicated that equilibrium isotopic fractionation occurred during ice segregation at the tree mounds, which implies that the ice formed with sufficient time for the migration of unfrozen soil water to the freezing front. In contrast, the isotopic data for the wet areas indicated that rapid freezing occurred under relatively non-equilibrium conditions, implying that there was insufficient time for ice segregation to occur. The freezing rate of the tree mounds was slower than that of the wet areas due to the difference of such as soil moisture and snow cover depends on vegetation and microtopography. These results indicate that future changes in snow cover, soil moisture, and organic layer, which control underground thermal conductivity, will have significant impacts on the freezing environment of the ground ice at the Taiga–Tundra boundary in northeastern Siberia. Such changes in the freezing environment will then affect vegetation due to changes in the microtopography of the ground surface. [ABSTRACT FROM AUTHOR]