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The interception of snow by the canopy is an important process in the water and energy balance in cold‐region coniferous forests. Direct measurements of canopy snow interception are difficult at scales larger than individual trees, requiring indirect methods such as eddy covariance, time‐lapse photography, or modeling. At the Niwot Ridge Subalpine Forest AmeriFlux site in the Colorado Front Range, USA, we compared methods that estimate or simulate the presence of snow interception. Timelapse photography images were analyzed using thresholding analysis and used to train a Convolutional Neural Network (CNN) model to estimate canopy snow presence. Interception was also estimated from eddy covariance measurements above and below the canopy, as well as from model simulations. These methods were applied over January 2019, with binarized results compared to a “ground truth” of human labeled images to calculate the Balanced Accuracy Score. The highest accuracy was achieved by the CNN predictions. Based on the Balanced Accuracy Scores, select methods were extended to estimate the presence of canopy snow for the 2018/2019 winter. All methods provided insight into the process of interception in a subalpine forest but presented challenges, including differing flux footprints of the above‐ and below‐canopy eddy covariance measurements and the inability of red‐green‐blue imagery to monitor snow interception at night, during sunrise, and during sunset. Key Points Snow interception in subalpine forests, identified via flux measurements, imagery and models, indicates its significance Convolutional Neural Network models trained with Phenocam imagery offer insights into snow interception beyond model development period Consider data availability and research goals when choosing a method to estimate the presence of snow interception

Understanding tree transpiration variability is vital for assessing ecosystem water‐use efficiency and forest health amid climate change, yet most landscape‐level measurements do not differentiate individual trees. Using canopy temperature data from thermal cameras, we estimated the transpiration rates of individual trees at Harvard Forest and Niwot Ridge. PT‐JPL model was used to derive latent heat flux from thermal images at the canopy‐level, showing strong agreement with tower measurements (R2 = 0.70–0.96 at Niwot, 0.59–0.78 at Harvard at half‐hourly to monthly scales) and daily RMSE of 33.5 W/m2 (Niwot) and 52.8 W/m2 (Harvard). Tree‐level analysis revealed species‐specific responses to drought, with lodgepole pine exhibiting greater tolerance than Engelmann spruce at Niwot and red oak showing heightened resistance than red maple at Harvard. These findings show how ecophysiological differences between species result in varying responses to drought and demonstrate that these responses can be characterized by deriving transpiration from crown temperature measurements. Plain Language Summary Understanding how forests use water, especially during droughts, is crucial for a changing climate. We developed a method using thermal cameras to estimate individual tree water loss (transpiration), something traditional methods lack. These cameras capture temperature data from the tree crown, which is then used to estimate transpiration rates. Tests in two forests showed this method aligns well with existing water use measurements. The study also revealed fascinating differences in how species handle drought. For instance, lodgepole pine outperformed Engelmann spruce in one forest, while red oak proved more resistant than red maple in the other. This shows that the thermal cameras can help assess how different trees resist drought conditions. This thermal camera technique has the potential to become a valuable tool for monitoring forest health as our climate evolves. Key Points Canopy‐level evapotranspiration derived from thermal cameras agreed well with eddy covariance measurements Crown temperature measurements facilitated the estimation of individual‐tree transpiration of co‐occurring species using the same approach The results show interspecific differences in water use and response to drought that align with species traits

The proliferation of digital cameras co-located with eddy covariance instrumentation provides new opportunities to better understand the relationship between canopy phenology and the seasonality of canopy photosynthesis. In this paper we analyze the abilities and limitations of canopy color metrics measured by digital repeat photography to track seasonal canopy development and photosynthesis, determine phenological transition dates, and estimate intra-annual and interannual variability in canopy photosynthesis. We used 59 site-years of camera imagery and net ecosystem exchange measurements from 17 towers spanning three plant functional types (deciduous broadleaf forest, evergreen needleleaf forest, and grassland/crops) to derive color indices and estimate gross primary productivity (GPP). GPP was strongly correlated with greenness derived from camera imagery in all three plant functional types. Specifically, the beginning of the photosynthetic period in deciduous broadleaf forest and grassland/crops and the end of the photosynthetic period in grassland/crops were both correlated with changes in greenness; changes in redness were correlated with the end of the photosynthetic period in deciduous broadleaf forest. However, it was not possible to accurately identify the beginning or ending of the photosynthetic period using camera greenness in evergreen needleleaf forest. At deciduous broadleaf sites, anomalies in integrated greenness and total GPP were significantly correlated up to 60 days after the mean onset date for the start of spring. More generally, results from this work demonstrate that digital repeat photography can be used to quantify both the duration of the photosynthetically active period as well as total GPP in deciduous broadleaf forest and grassland/crops, but that new and different approaches are required before comparable results can be achieved in evergreen needleleaf forest.

Recent successes in passive remote sensing of far-red solar-induced chlorophyll fluorescence (SIF) have spurred the development and integration of canopy-level fluorescence models in global terrestrial biosphere models (TBMs) for climate and carbon cycle research. The interaction of fluorescence with photochemistry at the leaf and canopy scales provides opportunities to diagnose and constrain model simulations of photosynthesis and related processes, through direct comparison to and assimilation of tower, airborne, and satellite data. TBMs describe key processes related to the absorption of sunlight, leaf-level fluorescence emission, scattering, and reabsorption throughout the canopy. Here, we analyze simulations from an ensemble of process-based TBM–SIF models (SiB3 – Simple Biosphere Model, SiB4, CLM4.5 – Community Land Model, CLM5.0, BETHY – Biosphere Energy Transfer Hydrology, ORCHIDEE – Organizing Carbon and Hydrology In Dynamic Ecosystems, and BEPS – Boreal Ecosystems Productivity Simulator) and the SCOPE (Soil Canopy Observation Photosynthesis Energy) canopy radiation and vegetation model at a subalpine evergreen needleleaf forest near Niwot Ridge, Colorado. These models are forced with local meteorology and analyzed against tower-based continuous far-red SIF and gross-primary-productivity-partitioned (GPP) eddy covariance data at diurnal and synoptic scales during the growing season (July–August 2017). Our primary objective is to summarize the site-level state of the art in TBM–SIF modeling over a relatively short time period (summer) when light, canopy structure, and pigments are similar, setting the stage for regional- to global-scale analyses. We find that these models are generally well constrained in simulating photosynthetic yield but show strongly divergent patterns in the simulation of absorbed photosynthetic active radiation (PAR), absolute GPP and fluorescence, quantum yields, and light response at the leaf and canopy scales. This study highlights the need for mechanistic modeling of nonphotochemical quenching in stressed and unstressed environments and improved the representation of light absorption (APAR), distribution of light across sunlit and shaded leaves, and radiative transfer from the leaf to the canopy scale.

Atmospheric models used for weather prediction and future climate projections rely on land models to calculate surface boundary conditions. Observations of near‐surface states and fluxes made at flux measurement sites provide valuable data with which to assess the quality of simulated lower boundary conditions. A previous assessment of the Community Land Model version 4.5 using data from the Niwot Ridge Subalpine Forest AmeriFlux tower showed that simulated latent heat fluxes could be improved by adjusting a parameter describing the maximum leaf wetted area, but biases in midday sensible heat flux and nighttime momentum flux were generally not reduced by model parameter perturbations. These biases are related to the model's lack of heat storage in vegetation biomass. A biomass heat capacity is parameterized in Community Land Model version 5 with measurable quantities such as canopy height, diameter at breast height, and tree number density. After implementing a parameterization describing the heat transfer between the forest biomass and the canopy air space, the biases in the mean midday sensible heat and mean nighttime momentum fluxes at Niwot Ridge are reduced from 47 to 13 W/m2 and from 0.12 to −0.03 m/s, respectively. The bias in the mean nighttime canopy air temperature was reduced from −5.9 to 0.4 °C. Additional simulations at other flux tower sites demonstrate a consistent reduction in midday sensible heat flux, a lower ratio of the sum of sensible and latent heat flux to net radiation, and an increase in nighttime canopy temperatures. Plain Language Summary Community Land Model exhibits a strong nighttime cold bias in surface temperature at forested sites. Representing the heat stored and released by vegetation biomass largely reduces this bias in the model, as well as biases in nighttime friction velocity and midday sensible heat flux. Key Points Simulations at forest sites exhibit nocturnal low bias of temperature and friction velocity, midday high bias of sensible heat Inclusion of biomass heat storage parameterization reduces these biases concurrently The parameterization shows similar positive impact across multiple sites with different plant functional types and climates

The Noah‐MP land surface model (LSM) relies on the Monin‐Obukhov (M‐O) Similarity Theory (MOST) to calculate land‐atmosphere exchanges of water, energy, and momentum fluxes. However, MOST flux‐profile relationships neglect canopy‐induced turbulence in the roughness sublayer (RSL) and parameterize within‐canopy turbulence in an ad hoc manner. We implement a new physics scheme (M‐O‐RSL) into Noah‐MP that explicitly parameterizes turbulence in RSL. We compare Noah‐MP simulations employing the M‐O‐RSL scheme (M‐O‐RSL simulations) and the default M‐O scheme (M‐O simulations) against observations obtained from 647 Snow Telemetry (SNOTEL) stations and two AmeriFlux stations in the western United States. M‐O‐RSL simulations of snow water equivalent (SWE) outperform M‐O simulations over 64% and 69% of SNOTEL sites in terms of root‐mean‐square‐error (RMSE) and correlation, respectively. The largest improvements in skill for M‐O‐RSL occur over closed shrubland sites, and the largest degradations in skill occur over deciduous broadleaf forest sites. Differences between M‐O and M‐O‐RSL simulated snowpack are primarily attributable to differences in aerodynamic conductance for heat underneath the canopy top, which modulates sensible heat flux. Differences between M‐O and M‐O‐RSL within‐canopy and below‐canopy sensible heat fluxes affect the amount of heat transported into snowpack and hence change snowmelt when temperatures are close to or above the melting point. The surface energy budget analysis over two AmeriFlux stations shows that differences between M‐O and M‐O‐RSL simulations can be smaller than other model biases (e.g., surface albedo). We intend for the M‐O‐RSL physics scheme to improve performance and uncertainty estimates in weather and hydrological applications that rely on Noah‐MP. Plain Language Summary Most widely used computer models of the land surface neglect canopy‐induced turbulence in calculations of heat, water, and momentum exchanges. Accounting for canopy‐induced turbulence is important because coherent eddies that form near the canopy top are responsible for generating most of the transportation of heat, water, and momentum, in and directly above the canopy. In 2007, 2008 scientists Ian N. Harman and John J. Finnigan developed a methodology that adapts contemporarily used equations in operational LSMs to account for canopy‐induced turbulence. In this study, we create a new physics option for the Noah with Multi‐Parameterization (Noah‐MP) LSM that accounts for canopy‐induced turbulence based on the Harman and Finnigan, 2007–2008 methodology. The primary focus of this study is to quantify differences between Noah‐MP snowpack simulations using the classical physics option that neglects canopy‐induced turbulence with the new physics option that accounts for canopy‐induced turbulence. Overall, simulations using the new physics option tend to have better agreement with ground‐based SWE observations across 647 validation sites within the western United States. We intend for the new physics scheme to improve weather and hydrological applications for operational modeling systems that rely on the Noah‐MP LSM. Key Points This study presents a new physics option for Noah‐MP that accounts for canopy‐induced turbulence in the roughness sublayer Simulated SWE over shrublands using the new turbulence scheme agree more with observations than those using the traditional MOST scheme Differences in snow simulations are mainly attributable to differences in aerodynamic resistance to sensible heat below the canopy top

Photosynthesis by terrestrial plants represents the majority of CO2 uptake on Earth, yet it is difficult to measure directly from space. Estimation of gross primary production (GPP) from remote sensing indices represents a primary source of uncertainty, in particular for observing seasonal variations in evergreen forests. Recent vegetation remote sensing techniques have highlighted spectral regions sensitive to dynamic changes in leaf/needle carotenoid composition, showing promise for tracking seasonal changes in photosynthesis of evergreen forests. However, these have mostly been investigated with intermittent field campaigns or with narrow-band spectrometers in these ecosystems. To investigate this potential, we continuously measured vegetation reflectance (400–900 nm) using a canopy spectrometer system, PhotoSpec, mounted on top of an eddy-covariance flux tower in a subalpine evergreen forest at Niwot Ridge, Colorado, USA. We analyzed driving spectral components in the measured canopy reflectance using both statistical and process-based approaches. The decomposed spectral components co-varied with carotenoid content and GPP, supporting the interpretation of the photochemical reflectance index (PRI) and the chlorophyll/carotenoid index (CCI). Although the entire 400–900 nm range showed additional spectral changes near the red edge, it did not provide significant improvements in GPP predictions. We found little seasonal variation in both normalized difference vegetation index (NDVI) and the near-infrared vegetation index (NIRv) in this ecosystem. In addition, we quantitatively determined needle-scale chlorophyll-to-carotenoid ratios as well as anthocyanin contents using full-spectrum inversions, both of which were tightly correlated with seasonal GPP changes. Reconstructing GPP from vegetation reflectance using partial least-squares regression (PLSR) explained approximately 87 % of the variability in observed GPP. Our results linked the seasonal variation in reflectance to the pool size of photoprotective pigments, highlighting all spectral locations within 400–900 nm associated with GPP seasonality in evergreen forests.

Most terrestrial carbon sequestration at mid-latitudes in the Northern Hemisphere occurs in seasonal, montane forest ecosystems. Winter respiratory carbon dioxide losses from these ecosystems are high, and over half of the carbon assimilated by photosynthesis in the summer can be lost the following winter. The amount of winter carbon dioxide loss is potentially susceptible to changes in the depth of the snowpack; a shallower snowpack has less insulation potential, causing colder soil temperatures and potentially lower soil respiration rates. Recent climate analyses have shown widespread declines in the winter snowpack of mountain ecosystems in the western USA and Europe that are coupled to positive temperature anomalies. Here we study the effect of changes in snow cover on soil carbon cycling within the context of natural climate variation. We use a six-year record of net ecosystem carbon dioxide exchange in a subalpine forest to show that years with a reduced winter snowpack are accompanied by significantly lower rates of soil respiration. Furthermore, we show that the cause of the high sensitivity of soil respiration rate to changes in snow depth is a unique soil microbial community that exhibits exponential growth and high rates of substrate utilization at the cold temperatures that exist beneath the snow. Our observations suggest that a warmer climate may change soil carbon sequestration rates in forest ecosystems owing to changes in the depth of the insulating snow cover.

Northern hemisphere evergreen forests assimilate a significant fraction of global atmospheric CO₂ but monitoring large-scale changes in gross primary production (GPP) in these systems is challenging. Recent advances in remote sensing allow the detection of solar-induced chlorophyll fluorescence (SIF) emission from vegetation, which has been empirically linked to GPP at large spatial scales. This is particularly important in evergreen forests, where traditional remote-sensing techniques and terrestrial biosphere models fail to reproduce the seasonality of GPP. Here, we examined the mechanistic relationship between SIF retrieved from a canopy spectrometer system and GPP at a winter-dormant conifer forest, which has little seasonal variation in canopy structure, needle chlorophyll content, and absorbed light. Both SIF and GPP track each other in a consistent, dynamic fashion in response to environmental conditions. SIF and GPP are well correlated (R² = 0.62–0.92) with an invariant slope over hourly to weekly timescales. Large seasonal variations in SIF yield capture changes in photoprotective pigments and photosystem II operating efficiency associated with winter acclimation, highlighting its unique ability to precisely track the seasonality of photosynthesis. Our results underscore the potential of new satellite-based SIF products (TROPOMI, OCO-2) as proxies for the timing and magnitude of GPP in evergreen forests at an unprecedented spatiotemporal resolution.

Understanding controls over plant-atmosphere CO₂ exchange is important for quantifying carbon budgets across a range of spatial and temporal scales. In this study, we used a simple approach to estimate whole-tree CO₂ assimilation rate (ATree) in a subalpine forest ecosystem. We analysed the carbon isotope ratio (δ¹³C) of extracted needle sugars and combined it with the daytime leaf-to-air vapor pressure deficit to estimate tree water-use efficiency (WUE). The estimated WUE was then combined with observations of tree transpiration rate (E) using sap flow techniques to estimate ATree. Estimates of ATree for the three dominant tree species in the forest were combined with species distribution and tree size to estimate and gross primary productivity (GPP) using an ecosystem process model. A sensitivity analysis showed that estimates of ATree were more sensitive to dynamics in E than δ¹³C. At the ecosystem scale, the abundance of lodgepole pine trees influenced seasonal dynamics in GPP considerably more than Engelmann spruce and subalpine fir because of its greater sensitivity of E to seasonal climate variation. The results provide the framework for a nondestructive method for estimating whole-tree carbon assimilation rate and ecosystem GPP over daily-to weekly time scales.