Toward a unified TreeTalker data curation process

The Internet of Things (IoT) development is revolutionizing environmental monitoring and research in macroecology. This technology allows for the deployment of sizeable diffuse sensing networks capable of continuous monitoring. Because of this property, the data collected from IoT networks can provide a testbed for scientific hypotheses across large spatial and temporal scales. Nevertheless, data curation is a necessary step to make large and heterogeneous datasets exploitable for synthesis analyses. This process includes data retrieval, quality assurance, standardized formatting, storage, and documentation. TreeTalkers are an excellent example of IoT applied to ecology. These are smart devices for synchronously measuring trees’ physiological and environmental parameters. A set of devices can be organized in a mesh and permit data collection from a single tree to plot or transect scale. The deployment of such devices over large-scale networks needs a standardized approach for data curation. For this reason, we developed a unified processing workflow according to the user manual. In this paper, we first introduce the concept of a unified TreeTalker data curation process. The idea was formalized into an R-package, and it is freely available as open software. Secondly, we present the different functions available in “ttalkR”, and, lastly, we illustrate the application with a demonstration dataset. With such a unified processing approach, we propose a necessary data curation step to establish a new environmental cyberinfrastructure and allow for synthesis activities across environmental monitoring networks. Our data curation concept is the first step for supporting the TreeTalker data life cycle by improving accessibility and thus creating unprecedented opportunities for TreeTalker-based macroecological analyse

New tree monitoring systems: from Industry 4.0 to Nature 4.0

Recently, Internet of Things (IoT) technologies have grown rapidly and represent now a unique opportunity to improve our environmental monitoring capabilities at extremely low costs. IoT is a new system of thinking in which objects, animals or people are equipped with unique identifiers and transfer data a network without requiring human-to-human or human-to-computer interaction. IoT has evolved from the convergence of wireless technologies, microelectromechanical systems (MEMS) and the Internet. The development of these technologies in environmental monitoring domains allows real-time data transmission and numerous low-cost monitoring points. We have designed a new device, the TreeTalker©, which is capable of measuring water transport in trees, diametrical growth, spectral characteristics of the leaves and microclimatic parameters and transmit data in semi-real time. Here we introduce the device’s features, provide an example of monitored data from a field test site and discuss the application of this new technology to tree monitoring in various contexts, from forest to urban green infrastructures management and ecological research

Continuous monitoring of tree responses to climate change for smart forestry: a cybernetic web of trees

6openBothTrees are long-lived organisms that contribute to forest development over centuries and beyond. However, trees are vulnerable to increasing natural and anthropic disturbances. Spatially distributed, continuous data are required to predict mortality risk and impact on the fate of forest ecosystems. In order to enable monitoring over sensitive and often remote forest areas that cannot be patrolled regularly, early warning tools/platforms of mortality risk need to be established across regions. Although remote sensing tools are good at detecting change once it has occurred, early warning tools require ecophysiological information that is more easily collected from single trees on the ground. Here, we discuss the requirements for developing and implementing such a treebased platform to collect and transmit ecophysiological forest observations and environmental measurements from representative forest sites, where the goals are to identify and to monitor ecological tipping points for rapid forest decline. Long-term monitoring of forest research plots will contribute to better understanding of disturbance and the conditions that precede it. International networks of these sites will provide a regional view of susceptibility and impacts and would play an important role in ground-truthing remotely sensed data.openTognetti, Roberto; Valentini, Riccardo; Belelli Marchesini, Luca; Gianelle, Damiano; Panzacchi, Pietro; Marshall, John D.Tognetti, R.; Valentini, R.; Belelli Marchesini, L.; Gianelle, D.; Panzacchi, P.; Marshall, J.D

Towards continuous stem water content and sap flux density monitoring: IoT-based solution for detecting changes in stem water dynamics

Taking advantage of novel IoT technologies, a new multifunctional device, the “TreeTalker”, was developed to monitor real-time ecophysical and biological parameters of individual trees, as well as climatic variables related to their surrounding environment, principally, air temperature and air relative humidity. Here, IoT applied to plant ecophysiology and hydrology aims to unravel the vulnerability of trees to climatic stress via a single tree assessment at costs that enable massive deployment. We present the performance of the TreeTalker to elucidate the functional relation between the stem water content in trees and respective internal/external (stem hydraulic activity/abiotic) drivers. Continuous stem water content records are provided by an in-house-designed capacitance sensor, hosted in the reference probe of the TreeTalker sap flow measuring system, based on the transient thermal dissipation (TTD) method. In order to demonstrate the capability of the TreeTalker, a three-phase experimental process was performed including (1) sensor sensitivity analysis, (2) sensor calibration, and (3) long-term field data monitoring. A negative linear correlation was demonstrated under temperature sensitivity analysis, and for calibration, multiple linear regression was applied on harvested field samples, explaining the relationship between the sample volumetric water content and the sensor output signal. Furthermore, in a field scenario, TreeTalkers were mounted on adult Fagus sylvatica L. and Quercus petraea L. trees, from June 2020 to October 2021, in a beech-dominated forest near Marburg, Germany, where they continuously monitored sap flux density and stem volumetric water content (stem VWC). The results show that the range of stem VWC registered is highly influenced by the seasonal variability of climatic conditions. Depending on tree characteristics, edaphic and microclimatic conditions, variations in stem VWC and reactions to atmospheric events occurred. Low sapwood water storage occurs in response to drought, which illustrates the high dependency of trees on stem VWC under water stress. Consistent daily variations in stem VWC were also clearly detectable. Stem VWC constitutes a significant portion of daily transpiration (using TreeTalkers, up to 4% for the beech forest in our experimental site). The diurnal–nocturnal pattern of stem VWC and sap flow revealed an inverse relationship. Such a finding, still under investigation, may be explained by the importance of water recharge during the night, likely due to sapwood volume changes and lateral water distribution rather than by a vertical flow rate. Overall, TreeTalker demonstrated the potential of autonomous devices for monitoring sap density and relative stem VWC in the field of plant ecophysiology and hydrolog

Studying the spatial variability of methane flux with five eddy covariance towers of varying height

In this study, the spatial representativeness of eddy covariance (EC) methane (CH4) measurements was examined by comparing parallel CH4 fluxes from three short (6 m) towers separated by a few kilometres and from two higher levels (20 m and 60 m) at one location. The measurement campaign was held on an intensively managed grassland on peat soil in the Netherlands. The land use and land cover types are to a large degree homogeneous in the area. The CH4 fluxes exhibited significant variability between the sites on 30-min scale. The spatial coefficient of variation (CVspa) between the three short towers was 56% and it was of similar magnitude as the temporal variability, unlike for the other fluxes (friction velocity, sensible heat flux) for which the temporal variability was considerably larger than the spatial variability. The CVspa decreased with temporal averaging, although less than what could be expected for a purely random process (1/√N), and it was 14% for 26-day means of CH4 flux. This reflects the underlying heterogeneity of CH4 flux in the studied landscape at spatial scales ranging from 1 ha (flux footprint) to 10 km2 (area bounded by the short towers). This heterogeneity should be taken into account when interpreting and comparing EC measurements. On an annual scale, the flux spatial variability contributed up to 50% of the uncertainty in CH4 emissions. It was further tested whether EC flux measurements at higher levels could be used to acquire a more accurate estimate of the spatially integrated CH4 emissions. Contrarily to what was expected, flux intensity was found to both increase and decrease depending on measurement height. Using footprint modelling, 56% of the variation between 6 m and 60 m CH4 fluxes was attributed to emissions from local anthropogenic hotspots (farms). Furthermore, morning hours proved to be demanding for the tall tower EC where fluxes at 60 m were up to four-fold those at lower heights. These differences were connected with the onset of convective mixing during the morning period.Peer reviewe

The Italian TREETALKER NETWORK (ITT-Net): continuous large scale monitoring of tree functional traits and vulnerabilities to climate change

20openItalian coauthor/editorThe Italian TREETALKER NETWORK (ITT-Net) aims to respond to one of the grand societal challenges: the impact of climate changes on forests ecosystem services and forest dieback. The comprehension of the link between these phenomena requires to complement the most classical approaches with a new monitoring paradigm based on large scale, single tree, high frequency and long-term monitoring tree physiology, which, at present, is limited by the still elevated costs of multi-sensor devices, their energy demand and maintenance not always suitable for monitoring in remote areas. The ITT-Net network will be a unique and unprecedented worldwide example of real time, large scale, high frequency and long-term monitoring of tree physiological parameters. By spring 2020, as part of a national funded project (PRIN) the network will have set 37 sites from the north-east Alps to Sicily where a new low cost, multisensor technology “the TreeTalker®” equipped to measure tree radial growth, sap flow, transmitted light spectral components related to foliage dieback and physiology and plant stability (developed by Nature 4.0), will monitor over 600 individual trees. A radio LoRa protocol for data transmission and access to cloud services will allow to transmit in real time high frequency data on the WEB cloud with a unique IoT identifier to a common database where big data analysis will be performed to explore the causal dependency of climate events and environmental disturbances with tree functionality and resilience. With this new network, we aim to create a new knowledge, introducing a massive data observation and analysis, about the frequency, intensity and dynamical patterns of climate anomalies perturbation on plant physiological response dynamics in order to: 1) characterize the space of “normal or safe tree operation mode” during average climatic conditions; 2) identify the non-linear tree responses beyond the safe operation mode, induced by extreme events, and the tipping points; 3) test the possibility to use a high frequency continuous monitoring system to identify early warning signals of tree stress which might allow to follow tree dynamics under climate change in real time at a resolution and accuracy that cannot always be provided through forest inventories or remote sensing technologies.openCastaldi, S.; Antonucci, S.; Asgharina, S.; Battipaglia, G.; Belelli Marchesini, L.; Cavagna, M.; Chini, I.; Cocozza, C.; Gianelle, D.; La Mantia, T.; Motisi, A.; Niccoli, F.; Pacheco Solana, A.; Sala, G.; Santopuoli, G.; Tonon, G.; Tognetti, R.; Zampedri, R.; Zorzi, I.; Valentini, R.Castaldi, S.; Antonucci, S.; Asgharina, S.; Battipaglia, G.; Belelli Marchesini, L.; Cavagna, M.; Chini, I.; Cocozza, C.; Gianelle, D.; La Mantia, T.; Motisi, A.; Niccoli, F.; Pacheco Solana, A.; Sala, G.; Santopuoli, G.; Tonon, G.; Tognetti, R.; Zampedri, R.; Zorzi, I.; Valentini, R

Geochemical, sedimentological and microbial diversity in two thermokarst lakes of far Eastern Siberia

Thermokarst lakes are important conduits for organic carbon sequestration, soil organic matter (soil-OM) decomposition and release of atmospheric greenhouse gases in the Arctic. They can be classified as either floating-ice lakes, which sustain a zone of unfrozen sediment (talik) at the lakebed year-round, or as bedfast-ice lakes, which freeze all the way to the lakebed in winter. Another key characteristic of thermokarst lakes are their eroding shorelines, depending on the surrounding landscape, they can play a major role in supplying the lakebeds with sediment and OM. These differences in winter ice regime and eroding shorelines are key factors which determine the quantity and quality of OM in thermokarst lake sediments. We used an array of physical, geochemical, and microbiological tools to identify the differences in the environmental conditions, sedimentary characteristics, carbon stocks and microbial community compositions in the sediments of a bedfast-ice and a floating-ice lake in Far East Siberia with different eroding shorelines. Our data show strong differences across most of the measured parameters between the two lakes. For example, the floating-ice lake contains considerably lower amounts of sediment organic matter and dissolved organic carbon, both of which also appear to be more degraded in comparison to the bedfast-ice lake, based on their stable carbon isotope composition (δ13C). We also document clear differences in the microbial community composition, for both archaea and bacteria. We identified the lake water depth (bedfast-ice vs. floating-ice) and shoreline erosion to be the two most likely main drivers of the sedimentary, microbial and biogeochemical diversity in thermokarst lakes. With ongoing climate warming, it is likely that an increasing number of lakes will shift from a bedfast- to a floating-ice state, and that increasing levels of shoreline erosion will supply the lakes with sediments. Yet, still little is known about the physical, biogeochemical and microbial differences in the sediments of these lake types and how different eroding shorelines impact these lake system

Methane flux measurements on multiple scales in an agricultural landscape: linking tall tower flux measurements with short eddy covariance towers

Agricultural landscapes exhibit spatially and temporally complex methane (CH4) fluxes: emissions originate from strong point sources, such as ruminants and cowsheds, and from fertilisation of fields, which adds short-term peaks in the methane flux to the atmosphere [1]. Furthermore, in some locations, such as the study site, these sources are overlaid on a CH4 flux originating from underlying peaty soils and drainage ditches between the fields [2]. In order to account for all these different sources, the CH4 fluxes need to be monitored continuously with a system that integrates the fluxes over a large area, providing the effective flux of CH4 from the landscape (~1 km2) to the atmosphere. Traditionally eddy covariance (EC) method has been used to obtain the ecosystem scale (~ 1 ha) fluxes of various compounds. However, it is questionable whether EC fluxes at one location can capture the high variability of CH4 fluxes in an agricultural landscape. To test this, methane exchange was measured at three locations with short (6.5 m high) EC towers a few kilometres apart from each other and at two heights (20 m and 60 m) in one tall tower. Additionally, it is assessed whether the short tower fluxes can be upscaled to match the CH4 fluxes measured at the tall tower using footprint modelling. The measurement campaign was held between the 1st and 25th of July 2012 in the vicinity of the Cabauw Experimental Site for Atmospheric Research (CESAR) (51°58’12.00”N, 4°55’34.48”E), which is located in the Netherlands. The landscape is an intensively managed agricultural area, with soil consisting of peat, topped by an approximately 1 meter thick bed of clay. Tentative results show large variability in CH4 fluxes between the three short tower sites: cumulative CH4 fluxes over a 10-day-period range from 188 mg(CH4) m-2 to 306 mg(CH4) m-2. Tall tower CH4 fluxes from the same period summed up to 275 mg(CH4) m-2 (20 m height) and 430 mg(CH4) m-2 (60 m height). High fluxes at 60 m height could be explained by cowsheds within the footprint, whereas systems located closer to the ground did not detect the hotspot emissions from the cowsheds. The presentation will discuss CH4 flux variability in an agricultural landscape, issues related to upscaling flux measurements and the usability of EC CH4 flux measurements at tall towers for estimating landscape scale exchange of methane. [1] P.S. Kroon et al., 2007, Biogeosciences, 4, 715-728. [2] A.P. Schrier-Uijl et al., 2010, Plant Soil, 329, 509-520

Evaluating the performance of commonly used gas analysers for methane eddy covariance flux measurements: the InGOS inter-comparison field experiment

The performance of eight fast-response methane (CH4) gas analysers suitable for eddy covariance flux measurements were tested at a grassland site near the Cabauw tall tower (Netherlands) during June 2012. The instruments were positioned close to each other in order to minimise the effect of varying turbulent conditions. The moderate CH4 fluxes observed at the location, of the order of 25 nmol m−2 s−1, provided a suitable signal for testing the instruments' performance. Generally, all analysers tested were able to quantify the concentration fluctuations at the frequency range relevant for turbulent exchange and were able to deliver high-quality data. The tested cavity ringdown spectrometer (CRDS) instruments from Picarro, models G2311-f and G1301-f, were superior to other CH4 analysers with respect to instrumental noise. As an open-path instrument susceptible to the effects of rain, the LI-COR LI-7700 achieved lower data coverage and also required larger density corrections; however, the system is especially useful for remote sites that are restricted in power availability. In this study the open-path LI-7700 results were compromised due to a data acquisition problem in our data-logging setup. Some of the older closed-path analysers tested do not measure H2O concentrations alongside CH4 (i.e. FMA1 and DLT-100 by Los Gatos Research) and this complicates data processing since the required corrections for dilution and spectroscopic interactions have to be based on external information. To overcome this issue, we used H2O mole fractions measured by other gas analysers, adjusted them with different methods and then applied them to correct the CH4 fluxes. Following this procedure we estimated a bias of the order of 0.1 g (CH4) m−2 (8% of the measured mean flux) in the processed and corrected CH4 fluxes on a monthly scale due to missing H2O concentration measurements. Finally, cumulative CH4 fluxes over 14 days from three closed-path gas analysers, G2311-f (Picarro Inc.), FGGA (Los Gatos Research) and FMA2 (Los Gatos Research), which were measuring H2O concentrations in addition to CH4, agreed within 3% (355–367 mg (CH4) m−2) and were not clearly different from each other, whereas the other instruments derived total fluxes which showed small but distinct differences (±10%, 330–399 mg (CH4) m−2).Peer reviewe