StrucNet: a global network for automated vegetation structure monitoring.

<p>Essential Biodiversity Variables (EBVs) are harmonized biodiversity variables and their asssociated measurements needed for developing indicators of global biodiversity change. EBVs can serve the important purpose of aligning biodiversity monitoring efforts, much as Essential Climatic Variables (ECVs) help align allied efforts in climate science. One of six initially proposed EBV classes is devoted to species' traits, since traits form the crucial link between the evolutionary history of organisms, their assembly into communities, and the nature and dynamic functioning of ecosystems. Despite their importance, prevalence, and scientific promise, the biodiversity community is still developing the conceptual, informatics, technical, and legal frameworks required for the large scale implementation and uptake. As part of an international consortium called GLOBIS-B, and in coordination with the The Group on Earth Observations Biodiversity Observation Network (GEO BON; geobon.org), we report on recent efforts to synthesize current efforts in trait data collection and trait datasets, computational workflows, ways to standardize data and metadata, and assessments of the openness and accessibility of existing species trait datasets. Members of the GLOBIS-B (www.globis-b.eu/) consortium also produced a set of candidate EBVs within the broader trait class ('Phenology', 'Organism morphology', 'Reproduction', 'Physiology' and 'Movement'). In this presentation, we begin by introducing the concept of EBVs, the current working definition of traits in the context of the EBV process, and workflows that have been developed for other EBV classes ('Species Populations') and the importance of standardizing EBV classes and the trait class, in particular. Building on this introduction, we discuss how the EBV concept is operationalized, focusing on workflows for trait integration, and the importance of data and metadata standards,following work from Kissling et al. 2017 (http://onlinelibrary.wiley.com/doi/10.1111/brv.12359/full). On the legal front, we suggest that the Creative Commons (CC) framework provides effective tools for designating legally interoperable and open data, especially when trait data are in the public domain (CC0, CC PDM) or assigned with a CC BY license, and metadata citation and other forms of attribution are available in both human and machine-readable form. We also suggest how EBVs can inform policy at national and global scales. Moving forward, renewed efforts of repeated trait data collection as well as standardised protocols for data and metadata collection are needed to improve the empirical basis of species traits EBVs. Moreover, open data as well as computational workflows are required for comprehensively assessing progress towards conservation policy targets and sustainable development goals. We conclude with a call to action for the TDWG community to consider their role in further developing, implementing, and scaling biodiversity monitoring under the EBV framework.</p>

Taking stock of nature: Essential biodiversity variables explained

The Earth system is enduring multiple, interacting stressors causing immense and irreversible change to its biosphere. The unprecedented magnitude of human influence on the planet is a cause for much concern, but also an opportunity to mitigate undesirable impact by instituting socio-ecological management strategies and monitoring their effectiveness. To do so, local and global policy developers and decision makers must have access to clear and globally consistent information streams that serve as planetary diagnostics. This need is being addressed by several international, multi-agency networks which have developed sets of "Essential Variables" (EVs) to improve consistency in the observation of key phenomena within their domains of operation. For example, the implementation of the Essential Climate Variables (ECVs) led by the Global Climate Observing System (GCOS) has set an example being followed in the marine and biodiversity domains by, respectively, the Global Ocean Observing System's (GOOS) Essential Ocean Variables (EOVs) and the Group on Earth Observation Biodiversity Observation Network (GEO BON)'s Essential Biodiversity Variables (EBVs). Each of these EV collections has a subset dedicated to biological and ecological phenomena. This is greatly encouraging for biodiversity science at large, but also runs the risk of parallel and conflicting developments occuring in the EV communities addressing thecross-cutting theme of biodiversity. As a consequence, there is an urgent need for these systems, and the communities behind them, to pursue tight conceptual and technical interoperability in aid of a coherent treatment of biodiversity in planetary-scale monitoring. In this contribution, we will describe our current research and implementation of a semantic interoperability layer for the EVs, with a focus on biology and ecology. Applying the best practices and core infrastructure of the Open Biological and Biomedical Ontology (OBO) Foundry and Library, we have leveraged both mature and emerging reference ontologies targeting the domains of ecosystems and environment, population and communities, and high-level ecological phenomena. This interoperable collection of ontologies constitutes a foundation for highly expressive EV knowledge representation and management through robust, FAIR-compliant technologies. Further, we are coordinating these efforts with semantic technology adopted by UN agencies, representing global directives and indicators of the UN Sustainable Development Agenda for 2030. With open editorial models behind each of these ontologies, we aim to offer a scalable and inclusive system to bridge data and information products across the EVs through machine-accessible knowledge representation.

The concept of Essential Biodiversity Variables (EBVs) for monitoring changes in biodiversity and tracking policy goals has substantially advanced in the last decade. I synthesize crucial information for developing an integrated European-wide biodiversity monitoring framework using EBVs to better inform environmental policies. This includes an overview of which EBVs have been prioritized for a modern and efficient European biodiversity observation network (Junker et al. 2023) and how these EBVs link to the EU policy framework and to different types of monitoring methods (Kissling et al. 2024). Generating EBVs requires designing and developing workflows for integrating primary observations from multiple data streams into aggregated and harmonized datasets that can then be modelled to derive spatially explicit EBV products with a specific spatial and temporal resolution (Kissling et al. 2018, Fernández et al. 2020). This requires information on data collection and sampling, data integration, and modelling for each EBV (Fig. 1). data collection and sampling, data integration, and modelling for each EBV (Fig. 1). To achieve this at a European scale, an improved data coverage, enhanced transnational coordination, adoption of advanced monitoring technologies, and a digital infrastructure with open data and interoperable standards is needed (Kissling et al. 2024, Moersberger et al. 2024, Morán-Ordóñez et al. 2023, Santana et al. 2023). To develop an effective EU-wide spatial sampling design, existing monitoring sites need to be incorporated, and spatial gaps need to be filled to achieve a broad representation of European biodiversity. This can be accomplished by combining a stratified random selection of sites (e.g. grid cells) across Europe with local sampling designs that consider randomisation, replication and stratification and co-location of monitoring activities using various field survey methods (Kissling et al. 2024). This can ensure a representative sampling across different environments, human impacts and policy or management interventions. Close collaborations between ecologists, data scientists, monitoring practitioners, and national and EU bodies, and the adoption of open science practices and FAIR guiding principles will be crucial to advance EBV implementation at a continental scale. This will support the establishment of a European Biodiversity Observation Coordination Centre (EBOCC) that is proposed for the coordination of monitoring activities and data management across Europe (Liquete et al. 2024).

Satellite remote sensing (SRS) provides huge potential for tracking progress towards conservation targets and goals, but SRS products need to be tailored towards the requirements of ecological users and policymakers. In this viewpoint article, we propose to advance SRS products with a terrestrial biodiversity focus for tracking the goals and targets of the Kunming-Montreal global biodiversity framework (GBF). Of 371 GBF biodiversity indicators, we identified 58 unique indicators for tracking the state of terrestrial biodiversity, spanning 2 goals and 8 targets. Thirty-six shared enough information to analyse their underlying workflows and spatial information products. We used the concept of Essential Biodiversity Variables (EBV) to connect spatial information products to different dimensions of biodiversity (e.g. species populations, species traits, and ecosystem structure), and then counted EBV usage across GBF goals and targets. Combined with published scores on feasibility, accuracy, and immaturity of SRS products, we identified a priority list of terrestrial SRS products representing opportunities for scientific development in the next decade. From this list, we suggest two key directions for advancing SRS products and workflows in the GBF context using current instruments and technologies. First, existing terrestrial ecosystem distributions and live cover fraction SRS products (of above-ground biomass, ecosystem fragmentation, ecosystem structural variance, fraction of vegetation cover, plant area index profile, and land cover) need to be refined using a co-design approach to achieve harmonized ecosystem taxonomies, reference states and improved thematic detail. Second, new SRS products related to plant physiology and primary productivity (e.g. leaf area index, chlorophyll content & flux, foliar N/P/K content, and carbon cycle) need to be developed to better estimate plant functional traits, especially with deep learning techniques, radiative transfer models and multi-sensor frameworks. Advancements along these two routes could greatly improve the tracking of GBF target 2 (‘improve connectivity of priority terrestrial ecosystems), target 3 (‘ensure management of protected areas’), target 6 (‘control the introduction and impact of invasive alien species’), target 8 (‘minimize impact of climate change on biodiversity’), target 10 (‘increase sustainable productivity of agricultural and forested ecosystems’) and target 12 (‘increase public urban green/blue spaces’). Such improvements can have secondary benefits for other EBVs, e.g. as predictor variables for modelling species distributions and population abundances (i.e. data that are required in several GBF indicators). We hope that our viewpoint stimulates the advancement of biodiversity monitoring from space and a stronger collaboration among ecologists, SRS scientists and policy experts.

Tree height is one of the key parameters for estimating forest aboveground biomass (AGB). Traditionally, the tree height is measured by hypsometers, which are widely used to validate terrestrial laser scanner (TLS) and Airborne LiDAR (ALS). However, the measurements from hypsometers are subject to huge uncertainties in comparison with TLS and ALS. The error associated with the height measurements propagate into the AGB estimation models, and eventually downgrade the accuracy of estimated AGB and the subsequent carbon stock. In this article, we test the use of hypsometer, TLS and ALS in a tropical lowland rainforest to measure the height (H) and diameter at breast height (DBH) and take Airborne LiDAR as a benchmark with high accuracy and fidelity in height measurements. The results revealed that, the field height measured by hypsometer underestimated the tree height with root-mean-square error (RMSE) of 3.11, whereas the TLS underestimated height with RMSE of 1.61, when Airborne LiDAR was used as a benchmark to validate the field measurement and TLS. Due to significant differences in derived height measurements, the AGB and carbon stock also varied remarkably with values of 146.33 and 68.77 Mg from field measurements, 170.86 and 80.31 Mg from TLS, 179.85 and 84.53 Mg using the Airborne LiDAR. Considering the Airborne LiDAR measurement as the most accurate, the AGB and carbon stock from field measurement represent 85.55% of total AGB and carbon stock estimation from Airborne LiDAR. Meanwhile, TLS measurements reflect 95.02% of AGB and carbon stock benchmarked with the measurements from Airborne LiDAR data. The results demonstrate the huge uncertainty in height measurement of large trees in comparison with small trees indicated by the significant differences. It was concluded that AGB and carbon stocks are sensitive to height measurement errors derived from various methods for measuring the tree height, the size of trees as large trees are difficult to measure height using hypsometer and TLS as opposed to small trees that are visible as well as the forest conditions. Compared with Airborne LiDAR, TLS achieved the higher accuracy of height estimation (R <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> = 0.91 with RMSE of 1.61) than the hypsometer (R <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> = 0.61 with RMSE of 3.11).

The concept of Essential Biodiversity Variables (EBVs) was conceived to study, report, and manage biodiversity change. The EBV netCDF structure was developed in order to support publication and interoperability of biodiversity data. This standard is based on the Network Common Data Format (netCDF). Additionally, it follows the Climate and Forecast Conventions (CF, version 1.8) and the Attribute Convention for Data Discovery (ACDD, version 1.3). The standard allows several datacubes per netCDF file (see Fig. 1). These cubes have four dimensions: longitude, latitude, time and entity, whereby the last dimension can, for example, encompass different species or groups of species, ecosystem types or other aspects. The usage of hierarchical groups enables the coexistence of multiple EBV cubes (see Fig. 2). The first level (netCDF group) are scenarios, e.g., the modelling for different Shared Socioeconomic Pathways (SSP) scenarios. The second level (netCDF group) are metrics, e.g., the percentage of protected area per pixel and its proportional loss over a certain time span per pixel. All metrics are repeated per scenario, if any are present. The result is a rather complex raster dataset (see example dataset in Fig. 3). This is where the ebvcube R package comes into play. This R package enables scientists to create their own netCDFs in the EBV cube standard. Its functionality covers the creation, opening/reading and visualizing the EBV netCDFs. The ebvcube package is part of the overall EBV infrastructure and works together with the EBV Data Portal. Users can work with the downloaded EBV netCDFs or upload their own EBV netCDFs to the portal. Generally, the package aims to condense the output for the users and assist in the understanding of the file structure to overcome the complexity. The output is reduced to the necessary information, e.g., not displaying coordinate variables or any technical attributes. Moreover, functionality for a quick data exploration is implemented.

Tropical forests host at least two-thirds of the world’s flora and fauna diversity and store 25% of the terrestrial above and belowground carbon. However, biodiversity decline due to deforestation and forest degradation of tropical forest is increasing at an alarming rate. Biodiversity dynamics due to natural and anthropogenic disturbances are mainly monitored using established field survey approaches. However, such approaches appear to fall short at addressing complex disturbance factors and responses. We argue that the integration of state-of-the-art monitoring approaches can improve the detection of subtle biodiversity disturbances and responses in changing tropical forests, which are often data-poor. We assess the state-of-the-art technologies used to monitor biodiversity dynamics of changing tropical forests, and how their potential integration can increase the detail and accuracy of biodiversity monitoring. Moreover, the relevance of these biodiversity monitoring techniques in support of the UNCBD Aichi targets was explored using the Essential Biodiversity Variables (EBVs) as a framework. Our review indicates that although established field surveys were generally the dominant monitoring systems employed, the temporal trend of monitoring approaches indicates the increasing application of remote sensing and in -situ sensors in detecting disturbances related to agricultural activities, logging, hunting and infrastructure. The relevance of new technologies (i.e., remote sensing, in situ sensors, and DNA barcoding) in operationalising EBVs (especially towards the ecosystem structure, ecosystem function, and species population classes) and the Aichi targets has been assessed. Remote sensing application is limited for EBV classes such as genetic composition and species traits but was found most suitable for ecosystem structure class. The complementarity of remote sensing and emerging technologies were shown in relation to EBV candidates such as species distribution, net primary productivity, and habitat structure. We also developed a framework based on the primary biodiversity attributes, which indicated the potential of integration between monitoring approaches. In situ sensors are suitable to help measure biodiversity composition, while approaches based on remote sensing are powerful for addressing structural and functional biodiversity attributes. We conclude that, synergy between the recent biodiversity monitoring approaches is important and possible. However, testing the suitability of monitoring methods across scales, integrating heterogeneous monitoring technologies, setting up metadata standards, and making interpolation and/or extrapolation from observation at different scales is still required to design a robust biodiversity monitoring system that can contribute to effective conservation measures.

The goal was to model irrigated (IBY) and rainfed (RBY) bean yields in central (Culiacán) and southern (Rosario) Sinaloa state as a function of the essential climate variables soil moisture, temperature, reference evapotranspiration, and precipitation. For Sinaloa, for the period 1982–2013 (October–March), the following were calculated: (a) temperatures, (b) average degree days for the bean, (c) cumulative reference evapotranspiration, and (d) cumulative effective precipitation. For essential climate variables, (e) daily soil moisture obtained from the European Space Agency and (f) IBY and RBY from the Agrifood and Fisheries Information Service were used. Multiple linear regressions were significant for predicting IBY–RBY (dependent variables) as a function of essential climate variables (independent variables). The four models obtained were significantly predictive: IBY–Culiacán (Pearson correlation (PC) = 0.590 &gt; Pearson critical correlation (CPC) = |0.349|), RBY–Culiacán (PC = 0.734 &gt; CPC = |0.349|), IBY–Rosario (PC = 0.621 &gt; CPC = |0.355|), and RBY–Rosario (PC = 0.532 &gt; CPC = |0.349|). Due to the lack of irrigation depth data, many studies only focus on modeling RBY; this study is the first in Sinaloa to predict IBY and RBY based on essential climate variables, contributing to the production of sustainable food.

Earth observation imaging technologies, particularly multispectral sensors, produce extensive high-dimensional data over time, thus offering a wealth of information on global dynamics. These data encapsulate crucial information in essential climate variables, such as varying levels of soil moisture and temperature. However, current cutting-edge machine learning models, including deep learning ones, often overlook the treasure trove of multidimensional data, thus analyzing each variable in isolation and losing critical interconnected information. In our study, we enhance conventional convolutional neural network models, specifically those based on the embedded temporal convolutional network framework, thus transforming them into models that inherently understand and interpret multidimensional correlations and dependencies. This transformation involves recasting the existing problem as a generalized case of N-dimensional observation analysis, which is followed by deriving essential forward and backward pass equations through tensor decompositions and compounded convolutions. Consequently, we adapt integral components of established embedded temporal convolutional network models, like encoder and decoder networks, thus enabling them to process 4D spatial time series data that encompass all essential climate variables concurrently. Through the rigorous exploration of diverse model architectures and an extensive evaluation of their forecasting prowess against top-tier methods, we utilize two new, long-term essential climate variables datasets with monthly intervals extending over four decades. Our empirical scrutiny, particularly focusing on soil temperature data, unveils that the innovative high-dimensional embedded temporal convolutional network model-centric approaches markedly excel in forecasting, thus surpassing their low-dimensional counterparts, even under the most challenging conditions characterized by a notable paucity of training data.

Temperate forests are crucial in global carbon dynamics, acting as significant carbon pools through biomass accumulation and soil organic matter storage. This study investigates the dynamics of the forest floor, soil organic matter, and carbon stock estimation on species type, age and forest management. The research focuses on Romania's temperate forests, on broadleaf, coniferous and mixed stands in the Southern Carpathians. The measurements were conducted across a systematic grid network of 450 plots, each combining two circular plots of 500 m&amp;#178; in size. These plots span an altitudinal gradient from 500 to 1650 meters above sea level (ASL), providing a robust dataset for analyzing carbon dynamics. Our research evaluates the contribution of forest floor components - litter, coarse woody debris and fine roots - to total carbon stocks, alongside soil organic matter dynamics at 30 cm depth. The study also integrates tree biomass data for major species such as beech (Fagus sylvatica L.), silver fir (Abies alba Mill. ), and Norway spruce (Picea abies L.), providing a comprehensive assessment of carbon sequestration potential.Our preliminary results reveal significant differences in both forest floor weight and bulk density between management types. Plots in conservation areas had a significantly higher mean forest floor weight (21.1 tonnes/ha) than production plots (17.9 tonnes/ha, p &lt; 0.01), while their mean bulk density was significantly lower (0.84 Mg/m&amp;#179; vs. 0.96 Mg/m&amp;#179;, p &lt; 0.01). These findings, combined with higher forest floor weight in conservation plots, underline the critical role of management strategies on soil carbon storage. The results also highlight the influence of forest type, stand age, and management practices on carbon storage, emphasizing their importance in climate change mitigation and sustainable forest management. This study provides valuable insights for optimizing forest management strategies to enhance carbon sequestration and improve understanding of carbon fluxes in temperate ecosystems. The findings are particularly relevant for aligning forest policies with national and international climate goals.

Accurate and up-to-date information concerning vegetation characteristics is needed for decision-making from individual-tree-level management activities to the strategic planning of forest resources. Outdated information may lead to unbeneficial or even wrong decisions, at least when it comes to the timing of management activities. Airborne laser scanning (ALS) has so far been successfully used for applications involving detailed vegetation mapping because of its capability to simultaneously produce accurate information on vegetation and ground surfaces. The aim of this dissertation was to develop methods for characterizing vegetation and its changes in varying environments. A method called multisource single-tree inventory (MS-STI) was developed in substudy I to update urban tree attributes. In MSSTI stem map was produced with terrestrial laser scanning and by combining the stem map with predictors derived from ALS data it was possible to obtain improved estimates of diameter-at-breast height but also to produce new attributes such as height and crown size. Boat-based mobile laser scanning (MLS) data were employed in substudy II to map riverbank vegetation and identify changes. The overall classification accuracy of 73% was obtained, which is similar to accuracies found in other studies. With multi-temporal MLS data sets changes in vegetation were mapped year to year. In substudy III, open access ALS data were combined with multisource national forest inventory (NFI) data to investigate the drivers associated to wind damage. The special interest was in ALS-based predictors to map areas with wind disturbance and apply logistic regression to produce a continuous probability surface of wind predisposition to identify areas most likely to experience wind damage. The results demonstrated that a combination of ALS and multisource NFI in the modelling approach increased the prediction accuracy from 76% to 81%. The dissertation showed the capability of ALS and MLS for characterizing vegetation and mapping changes in varying environments. The developed applications could increase and expand the utilization of multi-temporal 3D data sets as well as increase data value. The results of this dissertation can be utilized in producing more accurate, diverse, and up-to-date information for decision-making related to natural resources.

&amp;lt;jats:p&amp;gt;Within the last years terrestrial and airborne laser scanning has become a powerful technique for fast and efficient three-dimensional data acquisition of different kinds of objects. Airborne laser system (LiDAR) collects accurate georeferenced data of extremely large areas very quickly while the terrestrial laser scanner produces dense and geometrically accurate data. The combination of these two segments of laser scanning provides different areas of application. One of the applications is in the process of reconstruction of objects. Objects recorded with laser scanning technology and transferred into the final model represent the basis for building an object as it was original. In this paper, there will be shown two case studies based on usage of airborne and terrestrial laser scanning and processing of the data collected by them.&amp;lt;/jats:p&amp;gt;

Summary Vegetation structure is an important determinant of species habitats and diversity. It is often represented by simple metrics, such as canopy cover, height and leaf area index, which do not fully capture three‐dimensional variations in density. Terrestrial laser scanning (TLS) is a technology that can better capture vegetation structure, but methods developed to process scans have been biased towards forestry applications. The aim of this study was to develop a methodology for processing TLS data to produce vegetation density profiles across a broader range of habitats. We performed low‐resolution and medium‐resolution TLS scans using a Leica C5 Scanstation at four locations within eight sites near Wollongong, NSW, Australia (34·38–34·41°S, 150·84–150·91°E). The raw point clouds were converted to density profiles using a method that corrected for uneven ground surfaces, varying point density due to beam divergence and occlusion, the non‐vertical nature of most beams and for beams that passed through gaps in the vegetation without generating a point. Density profiles were evaluated against visual estimates from three independent observers using coarse height classes (e.g. 5–10 m). TLS produced density profiles that captured the three‐dimensional vegetation structure. Although sites were selected to differ in structure, each was relatively homogeneous, yet we still found a high spatial variation in density profiles. There was also large variation between observers, with the RMS error of the three observers relative to the TLS varying from 16·2% to 32·1%. Part of this error appeared to be due to misjudging the height of vegetation, which caused an overestimation in one height class and an underestimation in another. Our method for generating density profiles using TLS can capture three‐dimensional vegetation structure in a manner that is more detailed and less subjective than traditional methods. The method can be applied to a broad range of habitats – not just forests with open understoreys. However, it cannot accurately estimate near‐surface vegetation density when there are uneven surfaces or dense vegetation prevents sufficient ground returns. Nonetheless, TLS density profiles will be an important input for research on species habitats, microclimates and nutrient cycles.

In continuous cover forestry, plenter silviculture is regarded as an elaborated system for optimizing the sustainable production of high-quality timber maintaining a constant but heterogeneous canopy. Its complexity necessitates high silvicultural expertise and a detailed assessment of forest stand structural variables. Terrestrial laser scanning (TLS) can offer reliable techniques for long-term tree mapping, volume calculation, and stand variables assessment in complex forest structures. We conducted surveys using both automated TLS and conventional manual methods (CMM) on two plots with contrasting silvicultural regimes within the Black Forest, Germany. Variations in automated tree detection and stand variables were greater between different TLS surveys than with CMM. TLS detected an average of 523 tree stems per hectare, while CMM counted 516. Approximately 9.6% of trees identified with TLS were commission errors, with 6.5% of CMM trees being omitted using TLS. Basal area per hectare was slightly higher in TLS (38.9 m3) than in CMM (38.2 m3). However, CMM recorded a greater standing volume (492.7 m3) than TLS (440.5 m3). The discrepancy in stand volume between methods was primarily due to TLS underestimating tree height, especially for taller trees. DBH bias was minor at 1 cm between methods. Repeated TLS inventories successfully matched an average of 424 tree positions per hectare. While TLS adequately characterizes complex plenter forest structures, we propose enhancing this methodology with personal laser scanning to optimize crown coverage and efficiency and direct volume measurements for increased accuracy of wood volume estimations. Additionally, utilizing 3D point cloud data-derived metrics, such as structural complexity indices, can further enhance plenter forest management.