coveR: An R package for processing Digital Cover Photography images to retrieve forest canopy attributes

Digital Cover Photography (DCP) is an increasingly popular tool for estimating canopy cover and leaf area index (LAI). However, existing solutions to process canopy images are predominantly tailored for fisheye photography, whereas open-access tools for DCP are lacking. We developed an R package (coveR) to support the whole processing of DCP images in an automated, fast and reproducible way. The package functions, which are designed for step-by-step single-image analysis, can be performed sequentially in a pipeline and also allow simple implementation of batch-processing bunches of images. A case study is presented to demonstrate the reliability of canopy attributes derived from coveR in pure beech (Fagus sylvatica L.) stands with variable canopy density and structure. Estimates of gap fraction and effective LAI from DCP were validated against reference measurements obtained from terrestrial laser scanning. By providing a simple, transparent and flexible image processing procedure, coveR supported the use of DCP for routine measurements and monitoring of forest canopy attributes. This, combined with the implementability of DCP in many devices, including smartphones, micro-cameras, and remote trail cameras, can greatly expand the accessibility of the method also to non-experts.

Liquid Chromatographic/Mass Spectrometric Study on the Role of Beech (Fagus sylvatica L.) Wood Polyphenols in Red Heartwood Formation

The present research focused on the analysis of European beech (Fagus sylvatica L.) wood polyphenols in respect to red heartwood formation, which is a significant color and technological defect of the species. For the first time, high-performance liquid chromatography/tandem mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) were applied for the investigation of the structure and the radial distribution of polyphenols. Altogether 125 compounds were characterized by their MSn spectra, of which 71 were tentatively identified, including procyanidins (dimers to pentamers), flavonoids (taxifolin, naringenin, isorhamnetin, (epi)afzelechin), (+)-catechin, (–)-epicatechin) and their glycoside conjugates, phenolic acids (gallic acid, vanillic acid, syringic acid) and their glycosides as well as gallic acid derivatives, many of which were identified for the first time in beech wood. It was found that the concentration of many compounds increased at the color boundary. In situ polyphenol synthesis and metabolism were clearly evidenced at the color boundary. Red heartwood contained only free aglycones (syringic acid, taxifolin, naringenin, isorhamnetin, naringenin, syringic acid). Contrary to earlier assumptions, the MALDI-TOF analysis did not indicate the presence of oxidized high-molecular-weight polymeric polyphenols in the red heartwood tissues. The role of individual compounds in the formation of the red heartwood chromophores are discussed.

Biochemical markers in crop and forest species: a systematic review

Proteins and enzymes are informative biochemical markers frequently used in plant studies. The objective of this work was to present the studies with enzymes and proteins used as biochemical markers in crops and forest species—the articles prospected in the Scopus and Web of Science scientific databases in December 2020. The keywords were a combination of "agricultural" or "forest" with the Boolean operator and the enzymes' name: alcohol dehydrogenase/ADH, malate dehydrogenase/MDH, alpha-amylase/AMS, peroxiredoxin/PERX, and LEA proteins. Eighty-two articles addressed enzymes in agricultural or forest species were included in the analysis. The articles were published from 1976 to 2020, with an average annual publication of 12.2. Three hundred thirty-seven authors developed the annual percentage growth rate of 2.52% and articles. The most studied crops are Oryza sativa L., Glycine max L., Zea mays L., Hordeum vulgare L., specimens of the genera Triticum and Brassica. The forest species were Pinus, Picea, Nothofagus, Quercus, and Sorbus, and Fagus sylvatica L. The main tissues used for extraction are leaves, seeds, buds, and roots. The studies mainly deal with enzymes or proteins as markers associated with abiotic stresses and the structure or genetic diversity.

Health Condition of European Beech (Fagus sylvatica L.) According to Provenances in International Provenance Trial

The performance of European beech ( Fagus sylvatica L.) is severely threatened by abiotic and biotic stresses, but the resilience of its provenances from distinct geographic areas has not been sufficiently studied. Therefore, the performance of European beech was investigated in an international provenance trial consisting of twenty-one natural populations originating from Central Europe and Southeast Europe located on Medvednica Mountain (Croatia). The performance of European beech was investigated by characterizing I) damage types, II) crown damage intensity, III) damage frequency, and IV) clustering of provenances based on damage types. Anthracnose, galls, chewing damages, and aphids were recorded on leaves, and canker on the trunk and branches. The crown damage intensity was minute (less than 10%) for all types of disease. Anthracnose was the most common damage, followed in descending order by galls, canker, chewing damages and aphids. When the types of damage were analysed using descriptive statistics (frequency analysis and clustering), significant differences were recorded between provenances (χ2=322.19, p<0.0001). European beech provenances were classified into four clusters. Aphids and galls caused the least and the highest damage, respectively, in each cluster, except for Cluster 4, where anthracnose caused the highest damage. The results of this study showed generally good health condition of European beech provenances originating from Central and Southeast Europe in the period of the investigation.

Growth Recovery and Phenological Responses of Juvenile Beech (Fagus sylvatica L.) Exposed to Spring Warming and Late Spring Frost

Global change increases the risk of extreme climatic events. The impact of extreme temperature may depend on the tree species and also on the provenance. Ten provenances of Fagus sylvatica L. were grown in a common garden environment in Belgium and subjected to different temperature treatments. Half of the one year old seedlings were submitted to a high thermal stress in the spring of the first year, and all plants were exposed to a late spring frost in the second year. The high-temperature treated plants displayed reduced growth in the first year, which was fully compensated (recovery with exact compensation) in the second year for radial growth and in the third year for height growth. Frost in the spring of the second year damaged part of the saplings and reduced their growth. The frost damaged plants regained the pre-stress growth rate one year later (recovery without compensation). The high temperature treatment in the first year and the frost damage in the second year clearly influenced the phenological responses in the year of the event and in the succeeding year. Little population differentiation was observed among the provenances for growth and for phenological responses. Yet, a southern provenance, a non-autochthonous provenance (original German provenance that was planted in Belgium about a century ago) and a more continental provenance flushed earlier than the local Atlantic provenances in the year of the frost event, resulting in more frost damage. Some caution should therefore be taken when translocating provenances as an anticipation of the predicted climate warming.

Dynamics of Rare Earths and associated major and trace elements during Douglas-fir (Pseudotsuga menziesii) and European beech (Fagus sylvatica L.) litter degradation

Given the diverse physico-chemical properties of elements, we hypothesize that their incoherent distribution across the leaf tissues, combined with the distinct resistance to degradation that each tissue exhibits, leads to distinct turnover rates between elements. Moreover, litter layers of different ages produce diverse chemical signatures in solution during the wet degradation. To verify our hypothesis, Na, K, Mg, Mn, Ca, Pb, Al and Fe were analysed together with the Rare Earth Elements (REE) in the solid fractions and in the respective leachates of fresh leaves and different humus layers of two forested soils developed under Pseudotsuga menziesii and Fagus sylvatica L. trees. The results from the leaching experiment were also compared to the in situ REE composition of the soil solutions to clarify the impact that the litter degradation processes may have on soil solution chemical compositions. Our results clearly show that REE, Al, Fe and Pb were preferentially retained in the solid litter material, in comparison to the other cations, and that their concentrations increased over time during the litter degradation. Accordingly, different litter fractions produced different yields of elements and REE patterns in the leachates, indicating that the tree species and the age of the litter play a role in the chemical release during the degradation. In particular, the evolution of the REE patterns according to the age of the litter layers allowed us to deliver new findings on REE fractionation and mobilization during litter degradation. In particular, the LaN/YbN ratio highlights differences in litter degradation intensity between both tree species, which was not shown with major cations. We finally showed the primary control effect that litter degradation can have on the REE composition of the soil solution, which presents a positive Ce anomaly associated with the dissolution and/or transportation of Ce-enriched MnO2 particles accumulated onto the surface of the old litter due to white fungi activity. Similar MREE and HREE enrichments were also found in the leachates and the soil solution, probably due to their higher affinity to the organic acids, which represent the primary products from the organic matter degradation.