Using optical full-field measurement based on digital image correlation to measure strain on a tree subjected to mechanical load

Key message

The results indicate the usability of DIC technique in tree biomechanics is advantageous compared to standard procedure since it reveals the induced strain in full-field way, accurately and noninvasively.

Abstract

The goal of this study was to analyze and measure the displacement and strain response behavior of the tree (Juglans regia L.) subjected to a mechanical load. The analysis addresses issues of tree biomechanics that call for a high-quality deformation data measured on trees’ surfaces in a noninvasive way. For these purposes, the 3D digital image correlation (3D-DIC) was proposed and tested against standard extensometers. The measured tree was subjected to a bending by a pulling test to induce strain on the tree stem. The DIC technique successfully provided strain field on a tree bark despite its highly complicated geometry. Vertical averaging of the strain field obtained by the DIC revealed that a tree stem behaves according to beam theory exhibiting compression and tension parts. The absolute values of strain measured by both techniques agree with each other in order of magnitude, DIC returning lower values (approximately 21.1 and 40.8 % for compression and tension part, respectively). The results reveal necessity for future study of stress/strain transfer from xylem to bark. The sensitivity analysis shows that the computed strain highly depends on subset size used in the DIC computation. Based on the projection error and strain, the optimal subset size was found out to be between 21 and 31 pixels. The measurement proved that the DIC method can be successfully used in tree biomechanics. In general, our results and the character of DIC technique that allows testing at different scales depending on imaging methods indicate its big potential in plant biomechanics.     

Evaluating a non-destructive method for calibrating tree biomass equations derived from tree branching architecture

Key message

Functional branch analysis (FBA) is a promising non-destructive method that can produce accurate tree biomass equations when applied to trees which exhibit fractal branching architecture.

Abstract

Functional branch analysis (FBA) is a promising non-destructive alternative to the standard destructive method of tree biomass equation development. In FBA, a theoretical model of tree branching architecture is calibrated with measurements of tree stems and branches to estimate the coefficients of the biomass equation. In this study, species-specific and mixed-species tree biomass equations were derived from destructive sampling of trees in Western Kenya and compared to tree biomass equations derived non-destructively from FBA. The results indicated that the non-destructive FBA method can produce biomass equations that are similar to, but less accurate than, those derived from standard methods. FBA biomass prediction bias was attributed to the fact that real trees diverged from fractal branching architecture due to highly variable length–diameter relationships of stems and branches and inaccurate scaling relationships for the lengths of tree crowns and trunks assumed under the FBA model.     

NanoStriDE: normalization and differential expression analysis of NanoString nCounter data

Background

Relationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20^th century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21^st century.

Results

TreeRipper is a simple website for the fully-automated recognition of multifurcating phylogenetic trees (http://linnaeus.zoology.gla.ac.uk/~jhughes/treeripper/). The program accepts a range of input image formats (PNG, JPG/JPEG or GIF). The underlying command line c++ program follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line edges. The edge contour is then determined to detect the branch length, tip label positions and the topology of the tree. Optical Character Recognition (OCR) is used to convert the tip labels into text with the freely available tesseract-ocr software. 32% of images meeting the prerequisites for TreeRipper were successfully recognised, the largest tree had 115 leaves.

Conclusions

Despite the diversity of ways phylogenies have been illustrated making the design of a fully automated tree recognition software difficult, TreeRipper is a step towards automating the digitization of past phylogenies. We also provide a dataset of 100 tree images and associated tree files for training and/or benchmarking future software. TreeRipper is an open source project licensed under the GNU General Public Licence v3.     

Massive aerial roots affect growth and form of Dracaena draco

Key message

Large aerial roots grow out from the branches of injured Dracaena draco trees. They integrate with the trunk or cause the branches to break off the tree and deform it.

Abstract

Dracaena draco, the dragon tree, is an iconic monocot of the Canary Islands with a tree-like growth habit and some distinctive features that are unique in the plant kingdom. We report about the massive aerial roots in this tree. They appear on trees that are injured or under environmental stress and affect growth form and the whole life of the plant. We analysed the growth of these roots and tested our findings in experiments on plants. Clusters of these roots emerge from the bases of the lowest branches and growing down they may reach the soil. Descending along the trunk, they cling tightly to the trunk, integrate with it and contribute to its radial growth. This may explain (1) why the trunk of a mature D. draco tree looks fibrous, as if made of many individual strands, and (2) how some trees reach enormous radial dimensions. Alternately, a large, 2–5 m high, multi-segmented branch with aerial roots at its base, may break off the tree and grow on its own, as a mammoth off-cut, perhaps the largest known in the plant kingdom. This detachment would cause a significant reduction in the size of the crown and deform its original, highly organized pattern of branching. In the extreme condition this may result in the destruction of the mother plant.     

Assessment of nutrient removal in bearing peach trees (Prunus persica L. Batsch) based on whole tree analysis

Background and Aims

The aim was to assess the amounts of macro- (N, P, K, Ca and Mg) and micro-elements (Fe, Mn, Cu and Zn) lost by peach trees (Prunus persica L. Batsch) in all the nutrient removal events (pruning, flower abscission, fruit thinning, fruit harvest and leaf fall), as well as those stored in the permanent structures of the tree (roots, trunk and main branches).

Methods

Three peach cultivars were used. The biomass and nutrient composition of materials lost by trees at the different events were measured during 3 years. The biomass and nutrient composition of permanent tree structures were also measured after full tree excavation.

Results

Winter pruning and leaf fall were the events where most nutrients were removed. Nutrient losses and total requirements are given as amounts of nutrients needed per tree and also as amounts necessary to produce a t of fresh fruit.

Conclusions

The allocation of all nutrients analyzed in the different plant parts was similar in different types of peach trees, with each element having a typical “fingerprint” allocation pattern. Peach tree materials removed at tree pruning and leaf fall include substantial amounts of nutrients that could be recycled to improve soil fertility and tree nutrition. Poorly known tree materials such as flowers and fruit stones contain measurable amounts of nutrients.     

Is plant genetic control of ectomycorrhizal fungal communities an untapped source of stable soil carbon in managed forests?

Background

Ectomycorrhizal (ECM) fungi provide one of the main pathways for carbon (C) to move from trees into soils, where these fungi make significant contributions to microbial biomass and soil respiration.

Scope

ECM fungal species vary significantly in traits that likely influence C sequestration, such that forest C sequestration potential may be driven in part by the existing community composition of ECM fungi. Moreover, accumulating experimental data show that tree genotypes differ in their compatibility with particular ECM fungal species, i.e. mycorrhizal traits of forest trees are heritable. Those traits are genetically correlated with other traits for which tree breeders commonly select, suggesting that selection for traits of interest, such as disease resistance or growth rate, could lead to indirect selection for or against particular mycorrhizal traits of trees in forest plantations.

Conclusions

Altogether, these observations suggest that selection of particular tree genotypes could alter the community composition of symbiotic ECM fungi in managed forests, with cascading effects on soil functioning and soil C sequestration.     

Hydrological properties of bark of selected forest tree species. Part I: the coefficient of development of the interception surface of bark

Key message

The coefficient of development of the interception surface of bark allows for objective assessment of the degree of bark surface differentiation between different species.

Abstract

Inter-species differentiation of bark morphology and its variability progressing with tree age suggest that the hydrological properties of the bark of particular species depend on the degree of development of the outer bark surface of trees. The aim of the present research was to develop a method of calculating the actual bark surface with the use of the coefficient of development of the interception surface of bark, describing the degree of development of the outer bark surface of trees. The primary aim was to show inter-species differentiation of the coefficient of development of the interception surface of bark at breast height, as well as its variability within a single species, progressing with tree age. The present study shows the results obtained for 77 bark samples collected at the breast height of the following tree species: Pinus sylvestris L., Larix decidua Mill., Abies alba Mill., Picea abies L., Quercus robur L., Fagus sylvatica L., Acer pseudoplatanus L. and Betula pendula Ehrh. In all of the examined species, the coefficient of development of the interception surface of bark shows a distinct relation to the breast-height diameter. The highest values of coefficient of development of the interception surface of bark among the thickest trees are reached by: L. decidua—2.56, Pinus sylvestris—2.28 and B. pendula—2.44, whereas the lowest values are reached by the bark of European beech F. sylvatica—1.07. The coefficient of development of the interception surface of bark describes the morphological differentiation of the outer bark surface of trees in an objective way. Owing to its mathematical form, the coefficient of development of the interception surface of bark may be useful in the modelling of hydrological processes occurring in forest ecosystems.     

Tree-ring wood anatomy and stable isotopes show structural and functional adjustments in olive trees under different water availability

Background and Aims

Olive tree (Olea europaea L.) is a drought-tolerant tree species cultivated in Mediterranean-type environments. Although it is tolerant to drought, dry conditions decrease its productivity. A thorough analysis of the hydraulic architecture and wood anatomical plasticity, as well as of their physiological significance, is needed to understand how olive trees will adapt to the predicted increase in frequency and severity of drought in the Mediterranean region.

Methods

Dendrochronological, stable isotopic (δ¹³C, δ¹⁸O) and wood anatomical analyses were applied to understand how different water availability can affect wood stem structure and function, in rainfed and irrigated at 100 % of crop evapotranspiration (ETc) olive trees in an experimental orchard close to Benevento (Italy) from 1992 to 2009.

Results

Dendrochronological data indicate that cross-dating and synchronization of ring-width time series in olive tree is possible. After the start of irrigation, significantly more negative δ¹³C and lower δ¹⁸O values were recorded in irrigated trees indicating higher stomatal conductance and transpiration rates. Increased water balance induced the formation of a higher number of vessels with higher diameter.

Conclusions

Water balance variations affected wood anatomy and isotopic composition. Anatomical analyses detected structural and functional adjustments in rainfed trees that produced more vessels with lower diameter to prevent cavitation. Isotopic analyses confirmed that irrigated trees continuously showed enhanced transpiration rates.     

Spatial patterns of total and available N and P at alpine treeline

Background and aims

Vegetation can have direct and indirect effects on soil nutrients. To test the effects of trees on soils, we examined the patterns of soil nutrients and nutrient ratios at two spatial scales: at sites spanning the alpine tundra/subalpine forest ecotone (ecotone scale), and beneath and beyond individual tree canopies within the transitional krummholz zone (tree scale).

Methods

Soils were collected and analyzed for total carbon (C), nitrogen (N), and phosphorus (P) as well as available N and P on Niwot Ridge in the Colorado Rocky Mountains.

Results

Total C, N, and P were higher in the krummholz zone than the forest or tundra. Available P was also greatest in the krummholz zone while available N increased from the forest to the tundra. Throughout the krummholz zone, total soil nutrients and available P were higher downwind compared to upwind of trees.

Conclusions

The krummholz zone in general, and downwind of krummholz trees in particular, are zones of nutrient accumulation. This pattern indicates that the indirect effects of trees on soils are more important than the direct effects. The higher N:P ratios in the tundra suggest nutrient dynamics differ from the lower elevation sites. We propose that evaluating soil N and P simultaneously in soils may provide a robust assay of ecosystem nutrient limitation.     

Pre-treatment with salicylic acid induces phenolic responses of Norway spruce (<Emphasis Type="Italic">Picea abies</Emphasis>) bark to bark beetle (<Emphasis Type="Italic">Ips typographus</Emphasis>) attack

Keymessage

The temporal gradations of the investigated phenolics in Norway spruce bark after bark beetle (Ips typographus) attack followed the general eco-physiological concept. Treatment with salicylic acid inhibits bark beetle colonisation, alleviates the phenolic responses and activates the synthesis of condensed tannins on later sampling dates.

Abstract

Conifer bark is the target of numerous organisms due to its assimilated transport and nutrient storage functions. In the presented study, 100 mM salicylic acid (SA) was applied onto Norway spruce stems prior to being infested with bark beetles (Ips typographus L.), to study the temporal gradation of changes in condensed tannins (CT) and total phenolics (tPH) and their significance for mediating stress-tolerance. A significant accumulation of CT was monitored in untreated trees in response to progressive bark beetle infestation occurring from May onwards. In SA-treated infested trees, the CT values remained at control levels until May, but after the re-treatment of infested trees in June, the concentrations of CT rose significantly in comparison to the controls. The tPH values dropped 16 days after SA-treatment, independent of infestation, and later on remained at control level until July. In contrast, tPH contents accumulated in untreated infested trees in May, eased in June and increased again in July, when the trees were affected by the second generation of bark beetles. To sum up, in May and July when the highest beetle-flight activity was monitored the metabolic shift of phenolics within untreated infested trees differed significantly from the response of SA-treated trees. In addition, on SA-treated trees less entrance holes were monitored over the whole period of sampling when compared to untreated infested trees. These results provide evidence that SA-treatment alleviates the phenolic responses, activates the synthesis of condensed tannins and inhibits bark beetle colonisation.

     

Spatial distribution of the soil organic carbon pool in a Holm oak dehesa in Spain

Aims

Dehesas are agroforestry systems characterized by scattered trees among pastures, crops and/or fallows. A study at a Spanish dehesa has been carried out to estimate the spatial distribution of the soil organic carbon stock and to assess the influence of the tree cover.

Methods

The soil organic carbon stock was estimated from the five uppermost cm of the mineral soil with high spatial resolution at two plots with different grazing intensities. The Universal Kriging technique was used to assess the spatial distribution of the soil organic carbon stocks, using tree coverage within a buffering area as an auxiliary variable.

Results

A significant positive correlation between tree presence and soil organic carbon stocks up to distances of around 8 m from the trees was found. The tree crown cover within a buffer up to a distance similar to the crown radius around the point absorbed 30 % of the variance in the model for both grazing intensities, but residual variance showed stronger spatial autocorrelation under regular grazing conditions.

Conclusions

Tree cover increases soil organic carbon stocks, and can be satisfactorily estimated by means of crown parameters. However, other factors are involved in the spatial pattern of the soil organic carbon distribution. Livestock plays an interactive role together with tree presence in soil organic carbon distribution.     

<Emphasis Type="Italic">Mycoceros antennatissimus</Emphasis> gen. et sp. nov.: a mitosporic fungus capturing pollen grains

Mycoceros antennatissimus gen. et sp. nov. is described and illustrated from pollen grains deposited on the bark of Elaeagnus angustifolia and Platanus?×?acerifolia in Hungary. This fungus is shown to capture pollen grains by its three-dimensional shape. It clearly shows seasonality and appears to be rare. The following factors determine its ecological niche: (1) the availability of fresh Pinaceae pollen grains deposited from the air on the bark of a nearby standing angiosperm tree with (2) water-retaining spongious bark, and (3) rainy weather. Conidia are mainly dispersed by stemflow rainwater, while they hardly become airborne. Direct polymerase chain reaction (PCR) from single conidia made it possible to perform molecular phylogenetic investigation in order to clarify its taxonomic relationship within the Ascomycota.     

Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution

Background

Comparative genomic studies are revealing frequent gains and losses of whole genes via duplication and pseudogenization. One commonly used method for inferring the number and timing of gene gains and losses reconciles the gene tree for each gene family with the species tree of the taxa considered. Recent studies using this approach have found a large number of ancient duplications and recent losses among vertebrate genomes.

Results

I show that tree reconciliation methods are biased when the inferred gene tree is not correct. This bias places duplicates towards the root of the tree and losses towards the tips of the tree. I demonstrate that this bias is present when tree reconciliation is conducted on both multiple mammal and Drosophila genomes, and that lower bootstrap cut-off values on gene trees lead to more extreme bias. I also suggest a method for dealing with reconciliation bias, although this method only corrects for the number of gene gains on some branches of the species tree.

Conclusion

Based on the results presented, it is likely that most tree reconciliation analyses show biases, unless the gene trees used are exceptionally well-resolved and well-supported. These results cast doubt upon previous conclusions that vertebrate genome history has been marked by many ancient duplications and many recent gene losses.     

Precision and accuracy of tree-ring-based death dates of mountain pines in the Swiss National Park

Key message

Mountain pines in the Swiss National Park show evidence of partial cambial mortality, which affects the precision of tree-ring-based death dates, followed by lagged crown mortality.

Abstract

The time of tree death is commonly reconstructed by dating the outermost ring of tree-ring series. However, due to the occurrence of partial cambial mortality, the date of the outermost tree ring may vary between different locations on the tree stem. Furthermore, a tree may continue to live following the formation of the most recent tree ring. In this study, we quantified precision and accuracy of tree-ring-based death dates from 229 dead mountain pines (Pinus montana) from a 28 km² study area in the Swiss National Park. For almost two-thirds of the trees, a maximum difference of just 0–4 years between the dates of cambial mortality from three increment cores was observed, however, for a few trees the difference reached 30–65 years. Higher maximum differences between the dates of cambial mortality are expected for trees on steep slopes, for old trees or for trees that died a long time ago. For 84 % of dead mountain pines, which were sampled in a permanent sample plot with 2-year remeasurement intervals, the difference between the date of observed crown mortality and the death date determined from three cores was 0–5 years. Sampling two or just one core per tree decreases the accuracy of tree-ring-based death dates. Based on the findings of our study, we recommend a prior assessment of the precision and accuracy of tree-ring-based death dates for any dendroecological study dealing with the reconstruction of tree mortality.     

Soil organic C and nutrient contents under trees with different functional characteristics in seasonally dry tropical silvopastures

Aims

The selection of tree characteristics is critical for the outcome of the tree effects on soil fertility in silvopastoral pastures. This study aims to quantify the effects of trees on soil nutrient and C stocks, as well as assessing differences on the effects between legume (Albizia saman; Enterolobium cyclocarpum) and non-legume tree species (Tabebuia rosea; Guazuma ulmifolia).

Methods

In Central Nicaragua, soil was sampled (0–10 cm deep) in paired plots, under both a canopy and in open grassland, in 12 sites per tree species and analysed for organic C, total N stocks, available P and extractable K⁺, Ca²⁺ and Mg²⁺. To assess the effects of herbaceous composition and cattle to soil proprieties, we recorded the cover of plant groups and assessed the mass of dung in each plot.

Results

Soil organic C and N, available P and extractable K⁺ and Ca²⁺ were higher under the tree canopy than under paired open grassland. The basal area of trees was positively related with the canopy effect on soil variables, thus suggesting that the age or sizes of the trees are relevant factors associated with the content of soil C and nutrients. No specific effects related to the legume species group were detected.

Conclusions

Our results indicate that in fertile seasonally dry subtropical pastures, scattered trees have an overall effect on soil fertility, and that the magnitude of the effect depends more on the tree characteristics (i.e. basal area, crown area) than on whether the species is a legume or not.     

Constructing tree stem form from digitized surface measurements by a programming approach within discrete mathematics

Key message

The main message of this work is the demonstration of possibility of creation of stem shape from digitized points using integer-programming approach. The points are digitized by magnetic motion tracker which in contrast to the laser scanning allows the reconstruction of complete cross-section of stem even in the “hidden (invisible)” part.

Abstract

Three-dimensional information on tree stem form plays an important role in understanding the structure and strength of a standing tree against the forces of wind, snow, and other natural pressure. It also contributes to precision in volume measurement compared to conventional two-dimensional measurement. We investigate approaches for obtaining three-dimensional information of tree stem form from partially organized surface measurements, acquired using a three-dimensional digitizing device (Polhemus FASTRAK^® motion tracking device). We then propose a new programming approach from discrete mathematics to construct tree stem form. Our method is based on an optimal connection of neighbor triangles for surface construction, which is created by locally possible combination of three digitized points on the stem surface. We compare the proposed method to the existing heuristic methods of contour tracing and region growing. Our analysis shows that the proposed method provides a consistent construction of tree stem form, for even stems with extremely irregular structure such as those from bent trees and mangrove trees with unique root spread, while the other methods are incapable for constructing such tree stems.     

Sap flow-based quantitative indication of progression of Dutch elm disease after inoculation with Ophiostoma novo-ulmi

Key message

The rate of progression of Dutch elm disease can be continuously and quantitatively estimated from sap flow measurements.

Abstract

Response of sap flow to inoculation with Ophiostoma novo-ulmi, a causal agent which causes vascular mycosis called Dutch elm disease, was studied in a field experiment comprised of 4-year-old wych elm trees (Ulmus glabra). Sap flow was measured on inoculated trees using the trunk heat balance method with external heating (EMS 62, Czech Republic) throughout the experiment. The first detectable symptoms of reduction in sap flow occurred 6 days after inoculation and all inoculated trees died within 16 days. Our experiment confirmed the ability of O. novo-ulmi to quickly kill young elm trees. The disease progressed faster than in previous experiments utilizing O. ulmi. To the best of our knowledge, this is the first experiment using sap flow measurements on trees inoculated by O. novo-ulmi. The trunk heat balance sap flow method is an effective non-invasive tool for continuous quantitative monitoring of the progression of vascular tree diseases, and show increased potential for field and greenhouse studies on changes in xylem hydraulic conductivity in a wide range of broadleaved and coniferous tree species.