Leaf phenology amplitude derived from MODIS NDVI and EVI: maps of leaf phenology synchrony for Meso‐ and South America

The leaf phenology (i.e. the seasonality of leaf amount and leaf demography) of ecosystems can be characterized through the use of Earth observation data using a variety of different approaches. The most common approach is to derive time series of vegetation indices (VIs) which are related to the temporal evolution of FPAR, LAI and GPP or alternatively used to derive phenology metrics that quantify the growing season. The product presented here shows a map of average ‘amplitude’ (i.e. maximum minus minimum) of annual cycles observed in MODIS‐derived NDVI and EVI from 2000 to 2013 for Meso‐ and South America. It is a robust determination of the amplitude of annual cycles of vegetation greenness derived from a Lomb–Scargle spectral analysis of unevenly spaced data. VI time series pre‐processing was used to eliminate measurement outliers, and the outputs of the spectral analysis were screened for statistically significant annual signals. Amplitude maps provide an indication of net ecosystem phenology since the satellite observations integrate the greenness variations across the plant individuals within each pixel. The average amplitude values can be interpreted as indicating the degree to which the leaf life cycles of individual plants and species are synchronized. Areas without statistically significant annual variations in greenness may still consist of individuals that show a well‐defined annual leaf phenology. In such cases, the timing of the phenology events will vary strongly within the year between individuals. Alternatively, such areas may consist mainly of plants with leaf turnover strategies that maintain a constant canopy of leaves of different ages. Comparison with in situ observations confirms our interpretation of the average amplitude measure. VI amplitude interpreted as leaf life cycle synchrony can support model evaluation by informing on the likely leaf turn over rates and seasonal variation in ecosystem leaf age distribution

Leaf age effects on the spectral predictability of leaf traits in Amazonian canopy trees

Recent work has shown that leaf traits and spectral properties change through time and/or seasonally as leaves age. Current field and hyperspectral methods used to estimate canopy leaf traits could, therefore, be significantly biased by variation in leaf age. To explore the magnitude of this effect, we used a phenological dataset comprised of leaves of different leaf age groups -developmental, mature, senescent and mixed-age- from canopy and emergent tropical trees in southern Peru. We tested the performance of partial least squares regression models developed from these different age groups when predicting traits for leaves of different ages on both a mass and area basis. Overall, area-based models outperformed mass-based models with a striking improvement in prediction observed for area-based leaf carbon (Carea) estimates. We observed trait-specific age effects in all mass-based models while area-based models displayed age effects in mixed-age leaf groups for Parea and Narea. Spectral coefficients and variable importance in projection (VIPs) also reflected age effects. Both mass- and area-based models for all five leaf traits displayed age/temporal sensitivity when we tested their ability to predict the traits of leaves of other age groups. Importantly, mass based mature models displayed the worst overall performance when predicting the traits of leaves from other age groups. These results indicate that the widely adopted approach of using fully expanded mature leaves to calibrate models that estimate remotely-sensed tree canopy traits introduces error that can bias results depending on the phenological stage of canopy leaves. To achieve temporally stable models, spectroscopic studies should consider producing area-based estimates as well as calibrating models with leaves of different age groups as they present themselves through the growing season. We discuss the implications of this for surveys of canopies with synchronised and unsynchronised leaf phenology

Giant sequoia (Sequoiadendron giganteum) in the UK: carbon storage potential and growth rates

Giant sequoias (Sequoiadendron giganteum) are some of the UK's largest trees, despite only being introduced in the mid-nineteenth century. There are an estimated half a million giant sequoias and closely related coastal redwoods (Sequoia sempervirens) in the UK. Given the recent interest in planting more trees, partly due to their carbon sequestration potential and also their undoubted public appeal, an understanding of their growth capability is important. However, little is known about their growth and carbon uptake under UK conditions. Here, we focus on S. giganteum and use three-dimensional terrestrial laser scanning to perform detailed structural measurements of 97 individuals at three sites covering a range of different conditions, to estimate aboveground biomass (AGB) and annual biomass accumulation rates. We show that UK-grown S. giganteum can sequester carbon at a rate of 85 kg yr-1, varying with climate, management and age. We develop new UK-specific allometric models for S. giganteum that fit the observed AGB with r 2 > 0.93 and bias < 2% and can be used to estimate S. giganteum biomass more generally. This study provides the first estimate of the growth and carbon sequestration of UK open-grown S. giganteum and provides a baseline for estimating their longer-term carbon sequestration capacity

Convergence in relationships between leaf traits, spectra and age across diverse canopy environments and two contrasting tropical forests

• Leaf age structures the phenology and development of plants, as well as the evolution of leaf traits over life histories. However, a general method for efficiently estimating leaf age across forests and canopy environments is lacking. • Here, we explored the potential for a statistical model, previously developed for Peruvian sunlit leaves, to consistently predict leaf ages from leaf reflectance spectra across two contrasting forests in Peru and Brazil and across diverse canopy environments. • The model performed well for independent Brazilian sunlit and shade canopy leaves (R2 = 0.75–0.78), suggesting that canopy leaves (and their associated spectra) follow constrained developmental trajectories even in contrasting forests. The model did not perform as well for mid-canopy and understory leaves (R2 = 0.27–0.29), because leaves in different environments have distinct traits and trait developmental trajectories. When we accounted for distinct environment–trait linkages – either by explicitly including traits and environments in the model, or, even better, by re-parameterizing the spectra-only model to implicitly capture distinct trait-trajectories in different environments – we achieved a more general model that well-predicted leaf age across forests and environments (R2 = 0.79). • Fundamental rules, linked to leaf environments, constrain the development of leaf traits and allow for general prediction of leaf age from spectra across species, sites and canopy environments

TLS2trees: A scalable tree segmentation pipeline for TLS data

1. Above-ground biomass (AGB) is an important metric used to quantify the mass of carbon stored in terrestrial ecosystems. For forests, this is routinely estimated at the plot scale (typically 1 ha) using inventory measurements and allometry. In recent years, terrestrial laser scanning (TLS) has appeared as a disruptive technology that can generate a more accurate assessment of tree and plot scale AGB; however, operationalising TLS methods has had to overcome a number of challenges. One such challenge is the segmentation of individual trees from plot level point clouds that are required to estimate woody volume, this is often done manually (e.g. with interactive point cloud editing software) and can be very time consuming. / 2. Here we present TLS2trees, an automated processing pipeline and set of Python command line tools that aims to redress this processing bottleneck. TLS2trees consists of existing and new methods and is specifically designed to be horizontally scalable. The processing pipeline is demonstrated on 7.5 ha of TLS data captured across 10 plots of seven forest types; from open savanna to dense tropical rainforest. / 3. A total of 10,557 trees are segmented with TLS2trees: these are compared to 1281 manually segmented trees. Results indicate that TLS2trees performs well, particularly for larger trees (i.e. the cohort of largest trees that comprise 50% of total plot volume), where plot-wise tree volume bias is ±0.4 m3 and %RMSE is 60%. Segmentation performance decreases for smaller trees, for example where DBH ≤10 cm; a number of reasons are suggested including performance of semantic segmentation step. / 4. The volume and scale of TLS data captured in forest plots is increasing. It is suggested that to fully utilise this data for activities such as monitoring, reporting and verification or as reference data for satellite missions an automated processing pipeline, such as TLS2trees, is required. To facilitate improvements to TLS2trees, as well as modification for other laser scanning modes (e.g. mobile and UAV laser scanning), TLS2trees is a free and open-source software

Characterization of a Highly Biodiverse Floodplain Meadow Using Hyperspectral Remote Sensing within a Plant Functional Trait Framework

We assessed the potential for using optical functional types as effective markers to monitor changes in vegetation in floodplain meadows associated with changes in their local environment. Floodplain meadows are challenging ecosystems for monitoring and conservation because of their highly biodiverse nature. Our aim was to understand and explain spectral differences among key members of floodplain meadows and also characterize differences with respect to functional traits. The study was conducted on a typical floodplain meadow in UK (MG4-type, mesotrophic grassland type 4, according to British National Vegetation Classification). We compared two approaches to characterize floodplain communities using field spectroscopy. The first approach was sub-community based, in which we collected spectral signatures for species groupings indicating two distinct eco-hydrological conditions (dry and wet soil indicator species). The other approach was “species-specific”, in which we focused on the spectral reflectance of three key species found on the meadow. One herb species is a typical member of the MG4 floodplain meadow community, while the other two species, sedge and rush, represent wetland vegetation. We also monitored vegetation biophysical and functional properties as well as soil nutrients and ground water levels. We found that the vegetation classes representing meadow sub-communities could not be spectrally distinguished from each other, whereas the individual herb species was found to have a distinctly different spectral signature from the sedge and rush species. The spectral differences between these three species could be explained by their observed differences in plant biophysical parameters, as corroborated through radiative transfer model simulations. These parameters, such as leaf area index, leaf dry matter content, leaf water content, and specific leaf area, along with other functional parameters, such as maximum carboxylation capacity and leaf nitrogen content, also helped explain the species’ differences in functional dynamics. Groundwater level and soil nitrogen availability, which are important factors governing plant nutrient status, were also found to be significantly different for the herb/wetland species’ locations. The study concludes that spectrally distinguishable species, typical for a highly biodiverse site such as a floodplain meadow, could potentially be used as target species to monitor vegetation dynamics under changing environmental conditions

TLS2trees: A scalable tree segmentation pipeline for TLS data

1. Above-ground biomass (AGB) is an important metric used to quantify the mass of carbon stored in terrestrial ecosystems. For forests, this is routinely estimated at the plot scale (typically 1 ha) using inventory measurements and allometry. In recent years, terrestrial laser scanning (TLS) has appeared as a disruptive technology that can generate a more accurate assessment of tree and plot scale AGB; however, operationalising TLS methods has had to overcome a number of challenges. One such challenge is the segmentation of individual trees from plot level point clouds that are required to estimate woody volume, this is often done manually (e.g. with interactive point cloud editing software) and can be very time consuming. 2. Here we present TLS2trees, an automated processing pipeline and set of Python command line tools that aims to redress this processing bottleneck. TLS2treesconsists of existing and new methods and is specifically designed to be horizontally scalable. The processing pipeline is demonstrated on 7.5 ha of TLS data cap�tured across 10 plots of seven forest types; from open savanna to dense tropical rainforest. 3. A total of 10,557 trees are segmented with TLS2trees: these are compared to 1281 manually segmented trees. Results indicate that TLS2trees performs well, particularly for larger trees (i.e. the cohort of largest trees that comprise 50% of total plot volume), where plot-wise tree volume bias is ±0.4 m3 and %RMSE is 60%. Segmentation performance decreases for smaller trees, for example where DBH ≤10 cm; a number of reasons are suggested including performance of se�mantic segmentation step. 4. The volume and scale of TLS data captured in forest plots is increasing. It is sug�gested that to fully utilise this data for activities such as monitoring, reporting and verification or as reference data for satellite missions an automated processing pipeline, such as TLS2trees, is required. To facilitate improvements to TLS2trees, as well as modification for other laser scanning modes (e.g. mobile and UAV laser scanning), TLS2trees is a free and open-source software

Do dynamic global vegetation models capture the seasonality of carbon fluxes in the Amazon basin? A data-model intercomparison

© 2016 John Wiley & Sons Ltd To predict forest response to long-term climate change with high confidence requires that dynamic global vegetation models (DGVMs) be successfully tested against ecosystem response to short-term variations in environmental drivers, including regular seasonal patterns. Here, we used an integrated dataset from four forests in the Brasil flux network, spanning a range of dry-season intensities and lengths, to determine how well four state-of-the-art models (IBIS, ED2, JULES, and CLM3.5) simulated the seasonality of carbon exchanges in Amazonian tropical forests. We found that most DGVMs poorly represented the annual cycle of gross primary productivity (GPP), of photosynthetic capacity (Pc), and of other fluxes and pools. Models simulated consistent dry-season declines in GPP in the equatorial Amazon (Manaus K34, Santarem K67, and Caxiuanã CAX); a contrast to observed GPP increases. Model simulated dry-season GPP reductions were driven by an external environmental factor, ‘soil water stress’ and consequently by a constant or decreasing photosynthetic infrastructure (Pc), while observed dry-season GPP resulted from a combination of internal biological (leaf-flush and abscission and increased Pc) and environmental (incoming radiation) causes. Moreover, we found models generally overestimated observed seasonal net ecosystem exchange (NEE) and respiration (Re) at equatorial locations. In contrast, a southern Amazon forest (Jarú RJA) exhibited dry-season declines in GPP and Re consistent with most DGVMs simulations. While water limitation was represented in models and the primary driver of seasonal photosynthesis in southern Amazonia, changes in internal biophysical processes, light-harvesting adaptations (e.g., variations in leaf area index (LAI) and increasing leaf-level assimilation rate related to leaf demography), and allocation lags between leaf and wood, dominated equatorial Amazon carbon flux dynamics and were deficient or absent from current model formulations. Correctly simulating flux seasonality at tropical forests requires a greater understanding and the incorporation of internal biophysical mechanisms in future model developments

Dry‐Season Greening and Water Stress in Amazonia: The Role of Modeling Leaf Phenology

Large uncertainties on the sensitivity of Amazon forests to drought exist. Even though water stress should suppress photosynthesis and enhance tree mortality, a green‐up has been often observed during the dry season. This interplay between climatic forcing and forest phenology is poorly understood and inadequately represented in most of existing dynamic global vegetation models calling for an improved description of the Amazon seasonal dynamics. Recent findings on tropical leaf phenology are incorporated in the state‐of‐the‐art eco‐hydrological model Thetys & Chloris. The new model accounts for a mechanistic light‐controlled leaf development, synchronized dry‐season litterfall, and an age‐dependent leaf photosynthetic capacity. Simulation results from 32 sites in the Amazon basin over a 15‐year period successfully mimic the seasonality of gross primary productivity; evapotranspiration (ET); as well as leaf area index, leaf age, and leaf productivity. Representation of tropical leaf phenology reproduces the observed dry‐season greening, reduces simulated gross primary productivity, and does not alter ET, when compared with simulations without phenology. Tolerance to dry periods, with the exception of major drought events, is simulated by the model. Deep roots rather than leaf area index regulation mechanisms control the response to short‐term droughts, but legacy effects can exacerbate multiyear water stress. Our results provide a novel mechanistic approach to model leaf phenology and flux seasonality in the tropics, reconciling the generally observed dry‐season greening, ET seasonality, and decreased carbon uptake during severe droughts.Key PointsA mechanistic description of tropical leaf phenology for ecosystem models is presentedModel simulations for 32 sites in the Amazon realistically reproduce carbon/water fluxesLeaf phenology explains dry‐season greening with little impact on evapotranspiration fluxesPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/145345/1/jgrg21161_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/145345/2/jgrg21161-sup-0001-supplementary.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/145345/3/jgrg21161.pd