Hysteresis response of daytime net ecosystem exchange during drought

Continuous measurements of net ecosystem CO<sub>2</sub> exchange (NEE) using the eddy-covariance method were made over an agricultural ecosystem in the southeastern US. During optimum environmental conditions, photosynthetically active radiation (PAR) was the primary driver controlling daytime NEE, accounting for as much as 67 to 89% of the variation in NEE. However, soil water content became the dominant factor limiting the NEE-PAR response during the peak growth stage. NEE was significantly depressed when high PAR values coincided with very low soil water content. The presence of a counter-clockwise hysteresis of daytime NEE with PAR was observed during periods of water stress. This is a result of the stomatal closure control of photosynthesis at high vapor pressure deficit and enhanced respiration at high temperature. This result is significant since this hysteresis effect limits the range of applicability of the Michaelis-Menten equation and other related expressions in the determination of daytime NEE as a function of PAR. The systematic presence of hysteresis in the response of NEE to PAR suggests that the gap-filling technique based on a non-linear regression approach should take into account the presence of water-limited field conditions. Including this step is therefore likely to improve current evaluation of ecosystem response to increased precipitation variability arising from climatic changes

Calibration Strategies for Detecting Macroscale Patterns in NEON Atmospheric Carbon Isotope Observations

Carbon fluxes in terrestrial ecosystems and their response to environmental change are a major source of uncertainty in the modern carbon cycle. The National Ecological Observatory Network (NEON) presents the opportunity to merge eddy covariance (EC)-derived fluxes with CO2 isotope ratio measurements to gain insights into carbon cycle processes. Collected continuously and consistently across >40 sites, NEON EC and isotope data facilitate novel integrative analyses. However, currently provisioned atmospheric isotope data are uncalibrated, greatly limiting ability to perform cross-site analyses. Here, we present two approaches to calibrating NEON CO2 isotope ratios, along with an R package to calibrate NEON data. We find that calibrating CO2 isotopologues independently yields a lower δ13C bias (<0.05‰) and higher precision (<0.40‰) than directly correcting δ13C with linear regression (bias: <0.11‰, precision: 0.42‰), but with slightly higher error and lower precision in calibrated CO2 mole fraction. The magnitude of the corrections to δ13C and CO2 mole fractions vary substantially by site, underscoring the need for users to apply a consistent calibration framework to data in the NEON archive. Post-calibration data sets show that site mean annual δ13C correlates negatively with precipitation, temperature, and aridity, but positively with elevation. Forested and agricultural ecosystems exhibit larger gradients in CO2 and δ13C than other sites, particularly during the summer and at night. The overview and analysis tools developed here will facilitate cross-site analysis using NEON data, provide a model for other continental-scale observational networks, and enable new advances leveraging the isotope ratios of specific carbon fluxes. © 2021. The Authors.Open access articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Calibration Strategies for Detecting Macroscale Patterns in NEON Atmospheric Carbon Isotope Observations

Carbon fluxes in terrestrial ecosystems and their response to environmental change are a major source of uncertainty in the modern carbon cycle. The National Ecological Observatory Network (NEON) presents the opportunity to merge eddy covariance (EC)-derived fluxes with CO2 isotope ratio measurements to gain insights into carbon cycle processes. Collected continuously and consistently across >40 sites, NEON EC and isotope data facilitate novel integrative analyses. However, currently provisioned atmospheric isotope data are uncalibrated, greatly limiting ability to perform cross-site analyses. Here, we present two approaches to calibrating NEON CO2 isotope ratios, along with an R package to calibrate NEON data. We find that calibrating CO2 isotopologues independently yields a lower δ13C bias (<0.05‰) and higher precision (<0.40‰) than directly correcting δ13C with linear regression (bias: <0.11‰, precision: 0.42‰), but with slightly higher error and lower precision in calibrated CO2 mole fraction. The magnitude of the corrections to δ13C and CO2 mole fractions vary substantially by site, underscoring the need for users to apply a consistent calibration framework to data in the NEON archive. Post-calibration data sets show that site mean annual δ13C correlates negatively with precipitation, temperature, and aridity, but positively with elevation. Forested and agricultural ecosystems exhibit larger gradients in CO2 and δ13C than other sites, particularly during the summer and at night. The overview and analysis tools developed here will facilitate cross-site analysis using NEON data, provide a model for other continental-scale observational networks, and enable new advances leveraging the isotope ratios of specific carbon fluxes. © 2021. The Authors.Open access articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

eddy4R 0.2.0: a DevOps model for community-extensible processing and analysis of eddy-covariance data based on R, Git, Docker, and HDF5

Large differences in instrumentation, site setup, data format, and operating system stymie the adoption of a universal computational environment for processing and analyzing eddy-covariance (EC) data. This results in limited software applicability and extensibility in addition to often substantial inconsistencies in flux estimates. Addressing these concerns, this paper presents the systematic development of portable, reproducible, and extensible EC software achieved by adopting a development and systems operation (DevOps) approach. This software development model is used for the creation of the eddy4R family of EC code packages in the open-source R language for statistical computing. These packages are community developed, iterated via the Git distributed version control system, and wrapped into a portable and reproducible Docker filesystem that is independent of the underlying host operating system. The HDF5 hierarchical data format then provides a streamlined mechanism for highly compressed and fully self-documented data ingest and output. The usefulness of the DevOps approach was evaluated for three test applications. First, the resultant EC processing software was used to analyze standard flux tower data from the first EC instruments installed at a National Ecological Observatory (NEON) field site. Second, through an aircraft test application, we demonstrate the modular extensibility of eddy4R to analyze EC data from other platforms. Third, an intercomparison with commercial-grade software showed excellent agreement (R2  =  1.0 for CO2 flux). In conjunction with this study, a Docker image containing the first two eddy4R packages and an executable example workflow, as well as first NEON EC data products are released publicly. We conclude by describing the work remaining to arrive at the automated generation of science-grade EC fluxes and benefits to the science community at large. This software development model is applicable beyond EC and more generally builds the capacity to deploy complex algorithms developed by scientists in an efficient and scalable manner. In addition, modularity permits meeting project milestones while retaining extensibility with time