Thermal infrared (TIR) multi-/hyperspectral and sun-induced fluorescence (SIF) approaches together with classic solar-reflective (visible, near-, and shortwave infrared reflectance (VNIR)/SWIR) hyperspectral remote sensing form the latest state-of-the-art techniques for the detection of crop water stress. Each of these three domains requires dedicated sensor technology currently in place for ground and airborne applications and either have satellite concepts under development (e.g., HySPIRI/SBG (Surface Biology and Geology), Sentinel-8, HiTeSEM in the TIR) or are subject to satellite missions recently launched or scheduled within the next years (i.e., EnMAP and PRISMA (PRecursore IperSpettrale della Missione Applicativa, launched on March 2019) in the VNIR/SWIR, Fluorescence Explorer (FLEX) in the SIF). Identification of plant water stress or drought is of utmost importance to guarantee global water and food supply. Therefore, knowledge of crop water status over large farmland areas bears large potential for optimizing agricultural water use. As plant responses to water stress are numerous and complex, their physiological consequences affect the electromagnetic signal in different spectral domains. This review paper summarizes the importance of water stress-related applications and the plant responses to water stress, followed by a concise review of water-stress detection through remote sensing, focusing on TIR without neglecting the comparison to other spectral domains (i.e., VNIR/SWIR and SIF) and multi-sensor approaches. Current and planned sensors at ground, airborne, and satellite level for the TIR as well as a selection of commonly used indices and approaches for water-stress detection using the main multi-/hyperspectral remote sensing imaging techniques are reviewed. Several important challenges are discussed that occur when using spectral emissivity, temperature-based indices, and physically-based approaches for water-stress detection in the TIR spectral domain. Furthermore, challenges with data processing and the perspectives for future satellite missions in the TIR are critically examined. In conclusion, information from multi-/hyperspectral TIR together with those from VNIR/SWIR and SIF sensors within a multi-sensor approach can provide profound insights to actual plant (water) status and the rationale of physiological and biochemical changes. Synergistic sensor use will open new avenues for scientists to study plant functioning and the response to environmental stress in a wide range of ecosystems.

Volatile fatty acid intoxication (acidosis), a common process failure recorded in anaerobic reactors, leads to drastic losses in methane production. Unfortunately, little is known about the microbial mechanisms underlining acidosis and the potential to recover the process. In this study, triplicate mesophilic anaerobic reactors of 100 L were exposed to acidosis resulting from an excessive feeding with sugar beet pulp and were compared to a steady-state reactor. Stable operational conditions at the beginning of the experiment initially led to similar microbial populations in the four reactors, as revealed by 16S rRNA gene T-RFLP and high-throughput amplicon sequencing. Bacteroidetes and Firmicutes were the two dominant phyla, and although they were represented by a high number of operational taxonomic units, only a few were dominant. Once the environment became deterministic (selective pressure from an increased substrate feeding), microbial populations started to diverge between the overfed reactors. Interestingly, most of bacteria and archaea showed redundant functional adaptation to the changing environmental conditions. However, the dominant Bacteroidales were resistant to high volatile fatty acids content and low pH. The severe acidosis did not eradicate archaea and a clear shift in archaeal populations from acetotrophic to hydrogenotrophic methanogenesis occurred in the overfed reactors. After 11 days of severe acidosis (pH 5.2 ± 0.4), the process was quickly recovered (restoration of the biogas production with methane content above 50 %) in the overfed reactors, by adjusting the pH to around 7 using NaOH and NaHCO3. In this study we show that once the replicate reactors are confronted with sub-optimal conditions, their microbial populations start to evolve differentially. Furthermore the alterations of commonly used microbial parameters to monitor the process, such as richness, evenness and diversity indices were unsuccessful to predict the process failure. At the same time, we tentatively propose the replacement of the dominant Methanosaeta sp. in this case by Methanoculleus sp., to be a potential warning indicator of acidosis.

Detailed information from global remote sensing has greatly advanced ourunderstanding of Earth as a system in general and of agricultural processes in particular.Vegetation monitoring with global remote sensing systems over long time periods iscritical to gain a better understanding of processes related to agricultural change over longtime periods. This specifically relates to sub-humid to semi-arid ecosystems, whereagricultural change in grazing lands can only be detected based on long time series. Byintegrating data from different sensors it is theoretically possible to construct NDVI timeseries back to the early 1980s. However, such integration is hampered by uncertainties inthe comparability between different sensor products. To be able to rely on vegetationtrends derived from integrated time series it is therefore crucial to investigate whether vegetation trends derived from NDVI and phenological parameters are consistent acrossproducts. In this paper we analyzed several indicators of vegetation change for a range ofagricultural systems in Inner Mongolia, China, and compared the results across differentsatellite archives. Specifically, we compared two of the prime NDVI archives—AVHRR Global Inventory Modeling and Mapping Studies (GIMMS) and SPOT Vegetation (VGT)NDVI. Because a true accuracy assessment of long time series is not possible, we furthercompared SPOT VGT NDVI with NDVI from MODIS Terra as a benchmark. We foundhigh similarities in interannual trends, and also in trends of the seasonal amplitude andintegral between SPOT VGT and MODIS Terra (r > 0.9). However, we observedconsiderable disagreements in NDVI-derived trends between AVHRR GIMMS and SPOTVGT. We detected similar discrepancies for trends based on phenological parameters, suchas amplitude and integral of NDVI curves corresponding to seasonal vegetation cycles.Inconsistencies were partially related to land cover and vegetation density. Differentpre-processing schemes and the coarser spatial resolution of AVHRR GIMMS introducedfurther uncertainties. Our results corroborate findings from other studies that vegetationtrends derived from AVHRR GIMMS data not always reflect true vegetation changes. Amore thorough understanding of the factors introducing uncertainties in AVHRR GIMMStime series is needed, and we caution against using AVHRR GIMMS data in regionalstudies without applying regional sensitivity analyses.

High-resolution airborne thermal infrared (TIR) together with sun-induced fluorescence (SIF) and hyperspectral optical images (visible, near- and shortwave infrared; VNIR/SWIR) were jointly acquired over an experimental site. The objective of this study was to evaluate the potential of these state-of-the-art remote sensing techniques for detecting symptoms similar to those occurring during water stress (hereinafter referred to as ‘water stress symptoms’) at airborne level. Flights with two camera systems (Telops Hyper-Cam LW, Specim HyPlant) took place during 11th and 12th June 2014 in Latisana, Italy over a commercial grass (Festuca arundinacea and Poa pratense) farm with plots that were treated with an anti-transpirant agent (Vapor Gard^®; VG) and a highly reflective powder (kaolin; KA). Both agents affect energy balance of the vegetation by reducing transpiration and thus reducing latent heat dissipation (VG) and by increasing albedo, i.e., decreasing energy absorption (KA). Concurrent in situ meteorological data from an on-site weather station, surface temperature and chamber flux measurements were obtained. Image data were processed to orthorectified maps of TIR indices (surface temperature (T_s), Crop Water Stress Index (CWSI)), SIF indices (F₆₈₇, F₇₈₀) and VNIR/SWIR indices (photochemical reflectance index (PRI), normalised difference vegetation index (NDVI), moisture stress index (MSI), etc.). A linear mixed effects model that respects the nested structure of the experimental setup was employed to analyse treatment effects on the remote sensing parameters. Airborne T_s were in good agreement (∆T < 0.35 K) compared to in situ T_s measurements. Maps and boxplots of TIR-based indices show diurnal changes: T_s was lowest in the early morning, increased by 6 K up to late morning as a consequence of increasing net radiation and air temperature (T_air) and remained stable towards noon due to the compensatory cooling effect of increased plant transpiration; this was also confirmed by the chamber measurements. In the early morning, VG treated plots revealed significantly higher T_s compared to control (CR) plots (p = 0.01), while SIF indices showed no significant difference (p = 1.00) at any of the overpasses. A comparative assessment of the spectral domains regarding their capabilities for water stress detection was limited due to: (i) synchronously overpasses of the two airborne sensors were not feasible, and (ii) instead of a real water stress occurrence only water stress symptoms were simulated by the chemical agents. Nevertheless, the results of the study show that the polymer di-1-p-menthene had an anti-transpiring effect on the plant while photosynthetic efficiency of light reactions remained unaffected. VNIR/SWIR indices as well as SIF indices were highly sensitive to KA, because of an overall increase in spectral reflectance and thus a reduced absorbed energy. On the contrary, the TIR domain was highly sensitive to subtle changes in the temperature regime as induced by VG and KA, whereas VNIR/SWIR and SIF domain were less affected by VG treatment. The benefit of a multi-sensor approach is not only to provide useful information about actual plant status but also on the causes of biophysical, physiological and photochemical changes.

Land surface temperature (LST) is a fundamental parameter within the system of the Earth’s surface and atmosphere, which can be used to describe the inherent physical processes of energy and water exchange. The need for LST has been increasingly recognised in agriculture, as it affects the growth phases of crops and crop yields. However, challenges in overcoming the large discrepancies between the retrieved LST and ground truth data still exist. Precise LST measurement depends mainly on accurately deriving the surface emissivity, which is very dynamic due to changing states of land cover and plant development. In this study, we present an LST retrieval algorithm for the combined use of multispectral optical and thermal UAV images, which has been optimised for operational applications in agriculture to map the heterogeneous and diverse agricultural crop systems of a research campus in Germany (April 2018). We constrain the emissivity using certain NDVI thresholds to distinguish different land surface types. The algorithm includes atmospheric corrections and environmental thermal emissions to minimise the uncertainties. In the analysis, we emphasise that the omission of crucial meteorological parameters and inaccurately determined emissivities can lead to a considerably underestimated LST; however, if the emissivity is underestimated, the LST can be overestimated. The retrieved LST is validated by reference temperatures from nearby ponds and weather stations. The validation of the thermal measurements indicates a mean absolute error of about 0.5 K. The novelty of the dual sensor system is that it simultaneously captures highly spatially resolved optical and thermal images, in order to construct the precise LST ortho-mosaics required to monitor plant diseases and drought stress and validate airborne and satellite data.

Hyperspectral cameras onboard unmanned aerial vehicles (UAVs) have recently emerged for monitoring crop traits at the sub-field scale. Different physical, statistical, and hybrid methods for crop trait retrieval have been developed. However, spectra collected from UAVs can be confounded by various issues, including illumination variation throughout the crop growing season, the effect of which on the retrieval performance is not well understood at present. In this study, four retrieval methods are compared, in terms of retrieving the leaf area index (LAI), fractional vegetation cover (fCover), and canopy chlorophyll content (CCC) of potato plants over an agricultural field for six dates during the growing season. We analyzed: (1) The standard look-up table method (LUTstd), (2) an improved (regularized) LUT method that involves variable correlation (LUTreg), (3) hybrid methods, and (4) random forest regression without (RF) and with (RFexp) the exposure time as an additional explanatory variable. The Soil–Leaf–Canopy (SLC) model was used in association with the LUT-based inversion and hybrid methods, while the statistical modelling methods (RF and RFexp) relied entirely on in situ data. The results revealed that RFexp was the best-performing method, yielding the highest accuracies, in terms of the normalized root mean square error (NRMSE), for LAI (5.36%), fCover (5.87%), and CCC (15.01%). RFexp was able to reduce the effects of illumination variability and cloud shadows. LUTreg outperformed the other two retrieval methods (hybrid methods and LUTstd), with an NRMSE of 9.18% for LAI, 10.46% for fCover, and 12.16% for CCC. Conversely, LUTreg led to lower accuracies than those derived from RF for LAI (5.51%) and for fCover (6.23%), but not for CCC (16.21%). Therefore, the machine learning approaches—in particular, RF—appear to be the most promising retrieval methods for application to UAV-based hyperspectral data.