Simulation of Automatically Annotated Visible and Multi-/Hyperspectral Images Using the Helios 3D Plant and Radiative Transfer Modeling Framework.

Deep learning and multimodal remote and proximal sensing are widely used for analyzing plant and crop traits, but many of these deep learning models are supervised and necessitate reference datasets with image annotations. Acquiring these datasets often demands experiments that are both labor-intensive and time-consuming. Furthermore, extracting traits from remote sensing data beyond simple geometric features remains a challenge. To address these challenges, we proposed a radiative transfer modeling framework based on the Helios 3-dimensional (3D) plant modeling software designed for plant remote and proximal sensing image simulation. The framework has the capability to simulate RGB, multi-/hyperspectral, thermal, and depth cameras, and produce associated plant images with fully resolved reference labels such as plant physical traits, leaf chemical concentrations, and leaf physiological traits. Helios offers a simulated environment that enables generation of 3D geometric models of plants and soil with random variation, and specification or simulation of their properties and function. This approach differs from traditional computer graphics rendering by explicitly modeling radiation transfer physics, which provides a critical link to underlying plant biophysical processes. Results indicate that the framework is capable of generating high-quality, labeled synthetic plant images under given lighting scenarios, which can lessen or remove the need for manually collected and annotated data. Two example applications are presented that demonstrate the feasibility of using the model to enable unsupervised learning by training deep learning models exclusively with simulated images and performing prediction tasks using real images.

An arbuscular mycorrhizal fungus alters soil water retention and hydraulic conductivity in a soil texture specific way.

Arbuscular mycorrhizal fungi (AMF) alter plant water relations and contribute to soil structure. Although soil hydraulic properties depend on soil structure and may limit plant water uptake, little is known about how AMF influence soil water retention (the relation between the soil water content and soil water potential) and hydraulic conductivity in different soils. Instead, these soil hydraulic properties often are considered to be independent of AMF presence in experiments. We asked if this assumption holds true for both sand and loam. We grew maize plants either inoculated with Rhizophagus irregularis or with autoclaved inoculum in pots filled with quartz sand or loam soil until extraradical spread of the fungus throughout the pots was achieved. Each pot contained a hyphal compartment made of a soil sampling core (250 cm3) covered with a 20-µm nylon mesh to encourage fungus ingrowth but to exclude root ingrowth. We measured soil water retention and unsaturated hydraulic conductivity in these undisturbed root-free soil volumes. We observed that in loam harboring the mycorrhizal fungus, the soil water retention decreased, while in sand, it increased without detectable changes in the soil bulk density. The effects of the fungus on the soil water potential were strongest at low soil water contents in both soils. As a consequence of the altered water potentials in soils with the mycorrhizal fungus, soil hydraulic conductivity increased in loam but decreased in sand after fungus ingrowth. We conclude that in our study, the mycorrhizal fungus acted as a soil conditioner even distant from roots, which encouraged drainage in loams prone to sogginess but enhanced water storage in sands prone to quick desiccation. We recommend considering soil hydraulic properties as being dynamic in future studies on water relations of mycorrhizal plants.

Using leaf spectroscopy and pigment estimation to monitor indoor grown lettuce dynamic response to spectral light intensity.

Rising urban food demand is being addressed by plant factories, which aim at producing quality food in closed environment with optimised use of resources. The efficiency of these new plant production systems could be further increased by automated control of plant health and nutritious composition during cultivation, allowing for increased produce value and closer match between plant needs and treatment application with potential energy savings. We hypothesise that certain leaf pigments, including chlorophylls, carotenoids and anthocyanins, which are responsive to light, may be good indicator of plant performance and related healthy compounds composition and, that the combination of leaf spectroscopy and mathematical modelling will allow monitoring of plant cultivation through noninvasive estimation of leaf pigments. Plants of two lettuce cultivars (a green- and a red-leaf) were cultivated in hydroponic conditions for 18 days under white light spectrum in climate controlled growth chamber. After that period, plant responses to white light spectrum ('W') with differing blue wavelengths ('B', 420 - 450 nm) percentage (15% 'B15', and 40% 'B40') were investigated for a 14 days period. The two light spectral treatments were applied at photon flux densities (PFDs) of 160 and 240 µmol m-2 s-1, resulting in a total of four light treatments (160WB15, 160WB40, 240WB15, 240WB40). Chlorophyll a fluorescence measurements and assessment of foliar pigments, through destructive (in vitro) and non-destructive (in vivo) spectrophotometry, were performed at 1, 7 and 14 days after treatment initiation. Increase in measured and estimated pigments in response to WB40 and decrease in chlorophyll:carotenoid ratio in response to higher PFD were found in both cultivars. Cultivar specific behavior in terms of specific pigment content stimulation in response to time was observed. Content ranges of modelled and measured pigments were comparable, though the correlation between both needs to be improved. In conclusion, leaf pigment estimation may represent a potential noninvasive and real-time technique to monitor, and control, plant growth and nutritious quality in controlled environment agriculture.

A Photosynthetic Light Acclimation Model Accounting for the Effects of Leaf Age, Chlorophyll Content, and Intra-Leaf Radiation Transfer.

Mechanistic models of canopy photosynthesis usually upscale leaf photosynthesis to crop level. A detailed prediction of canopy microclimate with accurate leaf morphological and physiological model parameters is the pre-requisite for accurate predictions. It is well established that certain leaf model parameters (V cmax, J max) of the frequently adopted Farquhar and Caemmerer photosynthesis model change with leaf age and light interception history. Previous approaches to predict V cmax and J max focused primarily on light interception, either by cumulative intercepted photosynthetic photon flux density (PPFD) or by closely related proxy variables such as leaf nitrogen content per leaf area. However, for plants with monopodial growth, such as vertically grown tomatoes or cucumber crops, in greenhouse production, there is a strong relationship between leaf age and light interception, complicating the experimental and mathematical separation of both effects. We propose a modeling framework that separates age and light intensity-related acclimation effects in a crop stand: Improved approximation of intra-leaf light absorption profiles with cumulative chlorophyll content (Chl) is the basis, while parameters are estimated via Gaussian process regression from total Chl, carotenoid content (Car), and leaf mass per area (LMA). The model approximates light absorption profiles within a leaf and links them to leaf capacity profiles of photosynthetic electron transport. Published datasets for Spinacia oleracea and Eucalyptus pauciflora were used to parameterize the relationship between light and capacity profiles and to set the curvature parameter of electron transport rate described by a non-rectangular hyperbola on Cucumis sativus. Using the modified capacity and light absorption profile functions, the new model was then able to predict light acclimation in a 2-month period of a fully grown tomato crop. An age-dependent lower limit of the electron transport capacity per unit Chl was essential in order to capture the decline of V cmax and J max over time and space of the investigated tomato crop. We detected that current leaf photosynthetic capacity in tomato is highly affected by intercepted light-sum of 3-5 previous days.

Species-Specific Impact of Fusarium Infection on the Root and Shoot Characteristics of Asparagus.

Soil-borne pathogens can have considerable detrimental effects on asparagus (Asparagus officinalis) growth and production, notably caused by the Fusarium species F. oxysporum f.sp. asparagi, F. proliferatum and F. redolens. In this study, their species-specific impact regarding disease severity and root morphological traits was analysed. Additionally, various isolates were characterised based on in vitro physiological activities and on protein extracts using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS). The response of two asparagus cultivars to the different Fusarium species was evaluated by inoculating experiments. Differences in aggressiveness were observed between Fusarium species and their isolates on roots, while no clear disease symptoms became visible in ferns eight weeks after inoculation. F. redolens isolates Fred1 and Fred2 were the most aggressive strains followed by the moderate aggressive F. proliferatum and the less and almost non-aggressive F. oxysporum isolates, based on the severity of disease symptoms. Fungal DNA in stem bases and a significant induction of pathogenesis-related gene expression was detectable in both asparagus cultivars. A significant negative impact of the pathogens on the root characteristics total root length, volume, and surface area was detected for each isolate tested, with Fred1 causing the strongest effects. No significant differences between the tested asparagus cultivars were observed.

Atmospheric drought and low light impede mycorrhizal effects on leaf photosynthesis-a glasshouse study on tomato under naturally fluctuating environmental conditions.

Arbuscular mycorrhiza fungi (AMF) consume plant carbon and impact photosynthesis, but effects of AMF on plant gas exchange are transient and hardly predictable. This is at least partially because plant-internal nutrient-, water-, and sink-related effects, which can be influenced AMF, and atmospheric conditions integrate at the photosynthesis level. In nature and in plant production, plants face periodical and random short-term switches of environmental conditions that limit photosynthesis, which may impede stimulatory effects of AMF on leaf photosynthetic capacities. We hypothesized that mycorrhizal effects on plant internal-photosynthetic potentials will only translate to actual photosynthetic rates, if atmospheric conditions do not superimpose limitations to the photosynthetic process. We aimed to cover wide ranges of within and between-day variations in light intensities and vapor pressure deficits with an untargeted approach. We grew tomato plants hydroponically for 8 weeks in open pots and irrigated beyond pot water capacity every morning. Plants were inoculated or not with Funneliformis mosseae and were fertilized with a low-strength nutrient solution, which guaranteed good AMF colonization and comparable sets of mycorrhizal and non-mycorrhizal plants regarding developmental stage and leaf age. Instantaneous leaf photosynthesis was monitored continuously with transparent chambers during 3 days under naturally fluctuating greenhouse conditions on the two uppermost fully expanded leaves. We fitted mechanistic gas exchange models and modeled continuous daytime dynamics of net photosynthetic rates and stomatal conductance for representative sunlit canopies of random populations of mycorrhizal and non-mycorrhizal plants. Depending on time, mycorrhizal plants showed enhanced or decreased stomatal conductance over wide ranges of light intensities. Higher or lower stomatal opening in mycorrhizal plants became ineffective for photosynthetic rates under low light. In contrast and in accordance with the effects on stomatal conductance, photosynthetic rates were comparatively increased or decreased in mycorrhizal plants under high light conditions. This required at least moderate vapor pressure deficits. Under high atmospheric drought, stomatal conductance strongly declined in all plants, which also capped maximum photosynthetic rates under high light. Leaf photosynthetic capacities were higher in mycorrhizal plants when leaves contained more proteins and/or the plant-internal moisture stress was lower than in non-mycorrhizal plants. However, this only resulted in enhanced photosynthetic rates as long as leaves were not exposed to low radiation or high atmospheric drought. We conclude that light and atmospheric moisture are decisive factors for potential carbon cost and gain scenarios of plants associated with AMF.

Arbuscular Mycorrhizas: A Promising Component of Plant Production Systems Provided Favorable Conditions for Their Growth.

Arbuscular mycorrhizal (AM) fungi have become an attractive target as biostimulants in agriculture due to their known contributions to plant nutrient uptake and abiotic stress tolerance. However, inoculation with AM fungi can result in depressed, unchanged, or stimulated plant growth, which limits security of application in crop production systems. Crop production comprises high diversity and variability in atmospheric conditions, substrates, plant species, and more. In this review, we emphasize that we need integrative approaches for studying mycorrhizal symbioses in order to increase the predictability of growth outcomes and security of implementation of AM fungi into crop production. We briefly review known mechanisms of AM on nutrient uptake and drought tolerance of plants, on soil structure and soil hydraulic properties. We carve out that an important factor for both nutrient availability and drought tolerance is yet not well understood; the AM effects on soil hydraulic properties. We gave special emphasis to circular references between atmospheric conditions, soil hydraulic properties and plant nutrient and water uptake. We stress that interdisciplinary approaches are needed that account for a variability of atmospheric conditions and, how this would match to mycorrhizal functions and demands in a way that increased plant nutrient and water uptake can be effectively used for physiological processes and ultimately growth. Only with integrated analyses under a wide range of growing conditions, we will be able to make profound decisions whether or not to use AM in particular crop production systems or can adjust culture conditions in ways that AM plants thrive.

Arbuscular Mycorrhiza Improves Substrate Hydraulic Conductivity in the Plant Available Moisture Range Under Root Growth Exclusion.

Arbuscular mycorrhizal fungi (AMF) proliferate in soils and are known to affect soil structure. Although their contribution to structure is extensively investigated, the consequences of those processes for soil water extractability and transport has, so far, gained surprisingly little attention. Therefore we asked, whether AMF can affect water retention and unsaturated hydraulic conductivity under exclusion of root ingrowth, in order to minimize plant driven effects. We carried out experiments with tomato inoculated with Rhizoglomus irregulare in a soil substrate with sand and vermiculite that created variation in colonization by mixed pots with wild type (WT) plants and mycorrhiza resistant (RMC) mutants. Sampling cores were introduced and used to assess substrate moisture retention dynamics and modeling of substrate water retention and hydraulic conductivity. AMF reduced the saturated water content and total porosity, but maintained air filled porosity in soil spheres that excluded root ingrowth. The water content between field capacity and the permanent wilting point (6-1500 kPa) was only reduced in mycorrhizal substrates that contained at least one RMC mutant. Plant available water contents correlated positively with soil protein contents. Soil protein contents were highest in pots that possessed the strongest hyphal colonization, but not significantly affected. Substrate conductivity increased up to 50% in colonized substrates in the physiologically important water potential range between 6 and 10 kPa. The improvements in hydraulic conductivity are restricted to substrates where at least one WT plant was available for the fungus, indicating a necessity of a functional symbiosis for this effect. We conclude that functional mycorrhiza alleviates the resistance to water movement through the substrate in substrate areas outside of the root zone.

Arbuscular Mycorrhiza Alleviates Restrictions to Substrate Water Flow and Delays Transpiration Limitation to Stronger Drought in Tomato.

Arbuscular mycorrhizal fungi (AMF) proliferate in soil pores, on the surface of soil particles and affect soil structure. Although modifications in substrate moisture retention depend on structure and could influence plant water extraction, mycorrhizal impacts on water retention and hydraulic conductivity were rarely quantified. Hence, we asked whether inoculation with AMF affects substrate water retention, water transport properties and at which drought intensity those factors become limiting for plant transpiration. Solanum lycopersicum plants were set up in the glasshouse, inoculated or not with Funneliformis mosseae, and grown for 35 days under ample water supply. After mycorrhizal establishment, we harvested three sets of plants, one before (36 days after inoculation) and the second (day 42) and third (day 47) within a sequential drying episode. Sampling cores were introduced into pots before planting. After harvest, moisture retention and substrate conductivity properties were assessed and water retention and hydraulic conductivity models were fitted. A root water uptake model was adopted in order to identify the critical substrate moisture that induces soil derived transpiration limitation. Neither substrate porosity nor saturated water contents were affected by inoculation, but both declined after substrates dried. Drying also caused a decline in pot water capacity and hydraulic conductivity. Plant available water contents under wet (pF 1.8-4.2) and dry (pF 2.5-4.2) conditions increased in mycorrhizal substrates and were conserved after drying. Substrate hydraulic conductivity was higher in mycorrhizal pots before and during drought exposure. After withholding water from pots, higher substrate drying rates and lower substrate water potentials were found in mycorrhizal substrates. Mycorrhiza neither affected leaf area nor root weight or length. Consistently with higher substrate drying rates, AMF restored the plant hydraulic status, and increased plant transpiration when soil moisture declined. The water potential at the root surface and the resistance to water flow in the rhizosphere were restored in mycorrhizal pots although the bulk substrate dried more. Finally, substrates colonized by AMF can be more desiccated before substrate water flux quantitatively limits transpiration. This is most pronounced under high transpiration demands and complies with a difference of over 1,000 hPa in substrate water potential.

The Use of Features from Fluorescence, Thermography, and NDVI Imaging to Detect Biotic Stress in Lettuce.

Fluorescence, normalized difference vegetation index, and thermal imaging are three frequently used nondestructive methods to detect biotic stress in plants. Due, in part, to the inconsistent results reported in the literature and the lack of measurements on the whole-plant scale, we tested the suitability of a wide variety of variables obtained using these three imaging methods to classify young plants into biotically stressed and nonstressed plants. To this end, we applied the model plant-pathogen system lettuce-Rhizoctonia solani. The relevant data from each image and plant (healthy and diseased) was extracted semiautomatically using sophisticated image processing algorithms. This method enabled us to identify the most appropriate variables via discriminant function and logistic regression analysis: photosystem II maximum quantum yield (Fv/Fm) and fluorescence decline ratio can be used to classify variables with an error ≤0.052. Lettuce seedlings with an Fv/Fm ratio > 0.73 were consistently healthy. In some cases, it was possible to detect infection prior to the appearance of symptoms. Possibilities to transfer the method to horticultural practice are discussed.