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Research can be more transparent and collaborative by using Findable, Accessible, Interoperable, and Reusable (FAIR) principles to publish Earth and environmental science data. Reporting formats-instructions, templates, and tools for consistently formatting data within a discipline-can help make data more accessible and reusable. However, the immense diversity of data types across Earth science disciplines makes development and adoption challenging. Here, we describe 11 community reporting formats for a diverse set of Earth science (meta)data including cross-domain metadata (dataset metadata, location metadata, sample metadata), file-formatting guidelines (file-level metadata, CSV files, terrestrial model data archiving), and domain-specific reporting formats for some biological, geochemical, and hydrological data (amplicon abundance tables, leaf-level gas exchange, soil respiration, water and sediment chemistry, sensor-based hydrologic measurements). More broadly, we provide guidelines that communities can use to create new (meta)data formats that integrate with their scientific workflows. Such reporting formats have the potential to accelerate scientific discovery and predictions by making it easier for data contributors to provide (meta)data that are more interoperable and reusable.

Data standardization combined with descriptive metadata facilitate data reuse, which is the ultimate goal of the Findable, Accessible, Interoperable, and Reusable (FAIR) principles. Community data or metadata standards are increasingly created through an approach that emphasizes collaboration between various stakeholders. Such an approach requires platforms for collaboration on the development process that centers on sharing information and receiving feedback. Our objective in this study was to conduct a systematic review to identify data standards and reporting formats that use version control for developing data standards and to summarize common practices, particularly in earth and environmental sciences. Out of 108 data standards and reporting formats identified in our review, 32 used GitHub as the version control platform, and no other platforms were used. We found no universally accepted methodology for developing and publishing data standards. Many GitHub repositories did not use key features that could help developers to gather user feedback, or to create and revise standards that build on previous work. We provide guidance for community-driven standard development and associated documentation on GitHub based on a systematic review of existing practices.

Field observations of the soil-to-atmosphere CO2 flux—soil respiration, RS—are a prime example of ‘long tail’ data that historically have had neither centralized databases nor an agreed-upon reporting format. This has hindered scientific transparency, analytical reproducibility, and syntheses with respect to this globally-important component of the carbon cycle. Here we propose a new data and metadata reporting format for RS data, based on engagement with a wide range of researchers in the earth and ecological sciences as well as expert advisory panels. Our goal was a reporting format that would be relevant and useful for synthesis activities, optimizing data discoverability and usability while not placing an undue burden on data contributors. We describe previous RS data collection efforts, lessons learned from related databases and data-oriented networks (e.g., FLUXNET) in earth and ecological sciences, and the process of community consultation. The proposed reporting format focuses on chamber-level data and metadata, specifying measurement conditions and, for a given measurement period defined by beginning and ending timestamps, a mean RS flux (or CO2 concentration) and associated ancillary measurements. With input from the research community, we have also developed research data and metadata templates to support data collection adhering to the reporting format. Fundamentally, this format aims to enable findable, accessible, interoperable, and reusable data, while providing ‘future-proofing’ capabilities to support reanalyses using as yet unknown algorithms or approaches. This proposed RS reporting format is openly available online and is intended to be a dynamic document, subject to further community feedback and/or change.

Globally, soils store two to three times as much carbon as currently resides in the atmosphere, and it is critical to understand how soil greenhouse gas (GHG) emissions and uptake will respond to ongoing climate change. In particular, the soil-to-atmosphere CO2 flux, commonly though imprecisely termed soil respiration (RS ), is one of the largest carbon fluxes in the Earth system. An increasing number of high-frequency RS measurements (typically, from an automated system with hourly sampling) have been made over the last two decades; an increasing number of methane measurements are being made with such systems as well. Such high frequency data are an invaluable resource for understanding GHG fluxes, but lack a central database or repository. Here we describe the lightweight, open-source COSORE (COntinuous SOil REspiration) database and software, that focuses on automated, continuous and long-term GHG flux datasets, and is intended to serve as a community resource for earth sciences, climate change syntheses and model evaluation. Contributed datasets are mapped to a single, consistent standard, with metadata on contributors, geographic location, measurement conditions and ancillary data. The design emphasizes the importance of reproducibility, scientific transparency and open access to data. While being oriented towards continuously measured RS , the database design accommodates other soil-atmosphere measurements (e.g. ecosystem respiration, chamber-measured net ecosystem exchange, methane fluxes) as well as experimental treatments (heterotrophic only, etc.). We give brief examples of the types of analyses possible using this new community resource and describe its accompanying R software package.

Summary: Increasing seawater exposure is killing coastal trees globally, with expectations of accelerating mortality with rising sea levels. However, the impact of concomitant changes in atmospheric CO2 concentration, temperature, and vapor pressure deficit (VPD) on seawater‐induced tree mortality is uncertain.We examined the mechanisms of seawater‐induced mortality under varying climate scenarios using a photosynthetic gain and hydraulic cost optimization model validated against observations in a mature stand of Sitka spruce (Picea sitchensis) trees in the Pacific Northwest, USA, that were dying from recent seawater exposure.The simulations matched well with observations of photosynthesis, transpiration, nonstructural carbohydrates concentrations, leaf water potential, the percentage loss of xylem conductivity, and stand‐level mortality rates. The simulations suggest that seawater‐induced mortality could decrease by c. 16.7% with increasing atmospheric CO2 levels due to reduced risk of carbon starvation. Conversely, rising VPD could increase mortality by c. 5.6% because of increasing risk of hydraulic failure.Across all scenarios, seawater‐induced mortality was driven by hydraulic failure in the first 2 yr after seawater exposure began, with carbon starvation becoming more important in subsequent years. Changing CO2 and climate appear unlikely to have a significant impact on coastal tree mortality under rising sea levels. [ABSTRACT FROM AUTHOR]

The fortedata R package is an open data notebook from the Forest Resilience Threshold Experiment (FoRTE) – a modeling and manipulative field experiment that tests the effects of disturbance severity and disturbance type on carbon cycling dynamics in a temperate forest. Package data consist of measurements of carbon pools and fluxes and ancillary measurements to help analyze and interpret carbon cycling over time. Currently the package includes data and metadata from the first three FoRTE field seasons, serves as a central, updatable resource for the FoRTE project team, and is intended as a resource for external users over the course of the experiment and in perpetuity. Further, it supports all associated FoRTE publications, analyses, and modeling efforts. This increases efficiency, consistency, compatibility, and productivity while minimizing duplicated effort and error propagation that can arise as a function of a large, distributed and collaborative effort. More broadly, fortedata represents an innovative, collaborative way of approaching science that unites and expedites the delivery of complementary datasets to the broader scientific community, increasing transparency and reproducibility of taxpayer-funded science. The fortedata package is available via GitHub: https://github.com/FoRTExperiment/fortedata (last access: 19 February 2021), and detailed documentation on the access, used, and applications of fortedata are available at https://fortexperiment.github.io/fortedata/ (last access: 19 February 2021). The first public release, version 1.0.1 is also archived at 10.5281/zenodo.4399601 (Atkins et al., 2020b). All data products are also available outside of the package as.csv files: 10.6084/m9.figshare.13499148.v1 (Atkins et al., 2020c). [ABSTRACT FROM AUTHOR]

Soil respiration (Rs), the flow of CO2 from the soil surface to the atmosphere, is one of the largest carbon fluxes in the terrestrial biosphere. The spatial variability of Rs is both large and poorly understood, limiting our ability to robustly scale it in time and space. One factor in Rs spatial variability is the autotrophic contribution from plant roots, but it is uncertain how the proximity of plants affects the magnitude and temperature sensitivity of Rs. This study examined the effect of tree proximity on Rs in the growing and dormant seasons, as well as during moisture-limited times, in a temperate, coastal, deciduous forest in eastern Maryland, USA. In a linear mixed-effects model, tree basal area within 5 m (BA5) exerted a significant positive effect on the temperature sensitivity of soil respiration. Soil moisture was the dominant control on Rs during the dry portions of the year while soil moisture, temperature, and BA5 all exerted significant effects on Rs in wetter periods. Our results suggest that autotrophic respiration is more sensitive to temperature than heterotrophic respiration at these sites, although we did not measure these source fluxes directly, and that soil respiration is highly moisture-sensitive, even in a record-rainfall year. The Rs flux magnitudes (0.3-16.6 µmol m-2 s-1) and variability (coefficient of variability 10 %-22 % across plots) observed in this study were comparable to values observed over decades in similar forests. We estimate that four Rs observations were required to be within 50 % of the stand-level mean, and 311 to be within 5 %, at 90 % confidence. A better understanding of the spatial interactions between plants and microbes that results in measured Rs is necessary to link these processes with large scale soil-to-atmosphere C fluxes. [ABSTRACT FROM AUTHOR]

Increasing seawater exposure is killing coastal trees globally, with expectations of accelerating mortality with rising sea levels. However, the impact of concomitant changes in atmospheric CO 2 concentration, temperature, and vapor pressure deficit (VPD) on seawater-induced tree mortality is uncertain. We examined the mechanisms of seawater-induced mortality under varying climate scenarios using a photosynthetic gain and hydraulic cost optimization model validated against observations in a mature stand of Sitka spruce (Picea sitchensis) trees in the Pacific Northwest, USA, that were dying from recent seawater exposure. The simulations matched well with observations of photosynthesis, transpiration, nonstructural carbohydrates concentrations, leaf water potential, the percentage loss of xylem conductivity, and stand-level mortality rates. The simulations suggest that seawater-induced mortality could decrease by c. 16.7% with increasing atmospheric CO 2 levels due to reduced risk of carbon starvation. Conversely, rising VPD could increase mortality by c. 5.6% because of increasing risk of hydraulic failure. Across all scenarios, seawater-induced mortality was driven by hydraulic failure in the first 2 yr after seawater exposure began, with carbon starvation becoming more important in subsequent years. Changing CO 2 and climate appear unlikely to have a significant impact on coastal tree mortality under rising sea levels., (© 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation.)