In vivo spectroscopy and machine learning for the early detection and classification of different stresses in apple trees.

The use of in vivo spectroscopy to detect plant stress in its early stages has the potential to enhance food safety and reduce the need for plant protection products. However, differentiating between various stress types before symptoms appear remains poorly studied. In this study, we investigated the potential of Vis-NIR spectroscopy to differentiate between stress types in apple trees (Malus x domestica Borkh.) exposed to apple scab, waterlogging, and herbicides in a greenhouse. Using a spectroradiometer, we collected spectral signatures of leaves still attached to the tree and utilized machine learning techniques to develop predictive models for detecting stress presence and classifying stress type as early as 1-5 days after exposure. Our findings suggest that changes in spectral reflectance at multiple regions accurately differentiate various types of plant stress on apple trees. Our models were highly accurate (accuracies between 0.94 and 1) when detecting the general presence of stress at an early stage. The wavelengths important for classification relate to photosynthesis via pigment functioning (684 nm) and leaf water (~ 1800-1900 nm), which may be associated with altered gas exchange as a short-term stress response. Overall, our study demonstrates the potential of spectral technology and machine learning for early diagnosis of plant stress, which could lead to reduced environmental burden through optimizing resource utilization in agriculture.

Identification of spectral ranges that contribute to phytoplasma detection in apple trees - A step towards an on-site method.

'Candidatus Phytoplasma mali' is the bacterial agent associated with Apple Proliferation, a disease that causes high economic losses in affected commercial apple growing regions. The identification of the disease is carried out by visual inspection performed by skilled professionals in the orchards. To confirm an infection, costly molecular laboratory methods must be applied. Furthermore, both methods are very time-consuming. Here, we analysed the potential of a non-destructive method using in-field measurements to differentiate infected from non-infected apple trees (Malus domestica) based on spectral signatures of fresh leaves. By using multivariate statistics, we were able to distinguish infected from non-infected trees and identified the wavelengths relevant for the differentiation. Factors affecting the differentiation performance were the sampling date and bacterial colonization behaviour.

Fungicide-free management of Alternaria leaf blotch and fruit spot on apple indicates Alternaria spp. as secondary colonizer.

The fungal genus Alternaria is a pan-global pathogen of > 100 crops, and is associated with the globally expanding Alternaria leaf blotch in apple (Malus x domestica Borkh.) which leads to severe leaf necrosis, premature defoliation, and large economic losses. Up to date, the epidemiology of many Alternaria species is still not resolved as they can be saprophytic, parasitic or shift between both lifestyles and are also classified as primary pathogen able to infect healthy tissue. We argue that Alternaria spp. does not act as primary pathogen, but only as a necrosis-dependent opportunist. We studied the infection biology of Alternaria spp. under controlled conditions and monitored disease prevalence in real orchards and validated our ideas by applying fungicide-free treatments in 3-years field experiments. Alternaria spp. isolates were not able to induce necroses in healthy tissue, but only when prior induced damages existed. Next, leaf-applied fertilizers, without fungicidal effect, reduced Alternaria-associated symptoms (- 72.7%, SE: ± 2.5%) with the same efficacy as fungicides. Finally, low leaf magnesium, sulphur, and manganese concentrations were consistently linked with Alternaria-associated leaf blotch. Fruit spot incidence correlated positively with leaf blotch, was also reduced by fertilizer treatments, and did not expand during storage unlike other fungus-mediated diseases. Our findings suggest that Alternaria spp. may be a consequence of leaf blotch rather than its primary cause, as it appears to colonize the physiologically induced leaf blotch. Taking into account existing observations that Alternaria infection is connected to weakened hosts, the distinction may appear slight, but is of great significance, as we can now (a) explain the mechanism of how different stresses result in colonization with Alternaria spp. and (b) substitute fungicides for a basic leaf fertilizer. Therefore, our findings can result in significant decreases in environmental costs due to reduced fungicide use, especially if the same mechanism applies to other crops.

Organic and conservation agriculture promote ecosystem multifunctionality.

Ecosystems provide multiple services to humans. However, agricultural systems are usually evaluated on their productivity and economic performance, and a systematic and quantitative assessment of the multifunctionality of agroecosystems including environmental services is missing. Using a long-term farming system experiment, we evaluated and compared the agronomic, economic, and ecological performance of the most widespread arable cropping systems in Europe: organic, conservation, and conventional agriculture. We analyzed 43 agroecosystem properties and determined overall agroecosystem multifunctionality. We show that organic and conservation agriculture promoted ecosystem multifunctionality, especially by enhancing regulating and supporting services, including biodiversity preservation, soil and water quality, and climate mitigation. In contrast, conventional cropping showed reduced multifunctionality but delivered highest yield. Organic production resulted in higher economic performance, thanks to higher product prices and additional support payments. Our results demonstrate that different cropping systems provide opposing services, enforcing the productivity-environmental protection dilemma for agroecosystem functioning.

Tightly bound soil water introduces isotopic memory effects on mobile and extractable soil water pools.

Cryogenic vacuum extraction is the well-established method of extracting water from soil for isotopic analyses of waters moving through the soil-plant-atmosphere continuum. We investigate if soils can alter the isotopic composition of water through isotope memory effects, and determined which mechanisms are responsible for it. Soils with differing physicochemical properties were re-wetted with reference water and subsequently extracted by cryogenic water distillation. Results suggest some reference waters bind tightly to the soil and not all of this tightly bound water is removed during cryogenic vacuum extraction. Kinetic isotopic fractionation occurring when reference water binds to the soil is likely responsible for the 18O-depletion of re-extracted reference water, suggesting an enrichment of the tightly bound soil water pool. Further re-wetting of cryogenically extracted soils indicates an isotopic memory effect of tightly bound soil water on water added to the soil. The data suggest tightly bound soil water can influence the isotopic composition of mobile soil water. Findings show that soils influence the isotope composition of soil water by (i) kinetic fractionation when water is bound to the soil and (ii) equilibrium fractionation between different soil water pools. These findings could be relevant for plant water uptake investigations and complicate ecohydrological and paleohydrological studies.

No shift to a deeper water uptake depth in response to summer drought of two lowland and sub-alpine C3-grasslands in Switzerland.

Temperate C3-grasslands are of high agricultural and ecological importance in Central Europe. Plant growth and consequently grassland yields depend strongly on water supply during the growing season, which is projected to change in the future. We therefore investigated the effect of summer drought on the water uptake of an intensively managed lowland and an extensively managed sub-alpine grassland in Switzerland. Summer drought was simulated by using transparent shelters. Standing above- and belowground biomass was sampled during three growing seasons. Soil and plant xylem waters were analyzed for oxygen (and hydrogen) stable isotope ratios, and the depths of plant water uptake were estimated by two different approaches: (1) linear interpolation method and (2) Bayesian calibrated mixing model. Relative to the control, aboveground biomass was reduced under drought conditions. In contrast to our expectations, lowland grassland plants subjected to summer drought were more likely (43-68%) to rely on water in the topsoil (0-10 cm), whereas control plants relied less on the topsoil (4-37%) and shifted to deeper soil layers (20-35 cm) during the drought period (29-48%). Sub-alpine grassland plants did not differ significantly in uptake depth between drought and control plots during the drought period. Both approaches yielded similar results and showed that the drought treatment in the two grasslands did not induce a shift to deeper uptake depths, but rather continued or shifted water uptake to even more shallower soil depths. These findings illustrate the importance of shallow soil depths for plant performance under drought conditions.

Reliability and quality of water isotope data collected with a low-budget rain collector.

RATIONALE: Low-budget rain collectors for water isotope analysis, such as the 'ball-in-funnel type collector' (BiFC), are widely used in studies on stable water isotopes of rain. To date, however, an experimental quality assessment of such devices in relation to climatic factors does not exist. METHODS: We used Cavity Ring-Down Spectrometry (CRDS) to quantify the effects of evaporation on the δ(18)O values of reference water under controlled conditions as a function of the elapsed time between rainfall and collection for isotope analysis, the sample volume and the relative humidity (RH: 31% and 67%; 25 °C). The climate chamber conditions were chosen to reflect the warm and dry end of field conditions that favor evaporative enrichment (EE). We also tested the performance of the BiFC in the field, and compared our δ(2)H/δ(18)O data obtained by isotope ratio mass spectrometry (IRMS) with those from the Swiss National Network for the Observation of Isotopes in the Water Cycle (ISOT). RESULTS: The EE increased with time, with a 1‰ increase in the δ(18)O values after 10 days (RH: 25%; 25 °C; 35 mL (corresponding to a 5 mm rain event); p <0.001). The sample volume strongly affected the EE (max. value +1.5‰ for 7 mL samples (i.e., 1 mm rain events) after 72 h at 31% and 67% RH; p <0.001), whereas the relative humidity had no significant effect. Using the BiFC in the field, we obtained very tight relationships of the δ(2)H/δ(18)O values (r(2) ≥ 0.95) for three sites along an elevational gradient, not significantly different from that of the next ISOT station. CONCLUSIONS: Since the chosen experimental conditions were extreme compared with the field conditions, it was concluded that the BiFC is a highly reliable and inexpensive collector of rainwater for isotope analysis.

Iron acquisition by phytosiderophores contributes to cadmium tolerance.

Based on the ability of phytosiderophores to chelate other heavy metals besides iron (Fe), phytosiderophores were suggested to prevent graminaceous plants from cadmium (Cd) toxicity. To assess interactions between Cd and phytosiderophore-mediated Fe acquisition, maize (Zea mays) plants were grown hydroponically under limiting Fe supply. Exposure to Cd decreased uptake rates of 59Fe(III)-phytosiderophores and enhanced the expression of the Fe-phytosiderophore transporter gene ZmYS1 in roots as well as the release of the phytosiderophore 2'-deoxymugineic acid (DMA) from roots under Fe deficiency. However, DMA hardly mobilized Cd from soil or from a Cd-loaded resin in comparison to the synthetic chelators diaminetriaminepentaacetic acid and HEDTA. While nano-electrospray-high resolution mass spectrometry revealed the formation of an intact Cd(II)-DMA complex in aqueous solutions, competition studies with Fe(III) and zinc(II) showed that the formed Cd(II)-DMA complex was weak. Unlike HEDTA, DMA did not protect yeast (Saccharomyces cerevisiae) cells from Cd toxicity but improved yeast growth in the presence of Cd when yeast cells expressed ZmYS1. When supplied with Fe-DMA as a Fe source, transgenic Arabidopsis (Arabidopsis thaliana) plants expressing a cauliflower mosaic virus 35S-ZmYS1 gene construct showed less growth depression than wild-type plants in response to Cd. These results indicate that inhibition of ZmYS1-mediated Fe-DMA transport by Cd is not related to Cd-DMA complex formation and that Cd-induced phytosiderophore release cannot protect maize plants from Cd toxicity. Instead, phytosiderophore-mediated Fe acquisition can improve Fe uptake in the presence of Cd and thereby provides an advantage under Cd stress relative to Fe acquisition via ferrous Fe.