Spatiotemporal alignment of radial tracheid diameter profiles of submontane Norway spruce

Studying intra-annual wood formation dynamics provides valuable information on how tree growth and forests are affected by environmental changes and climatic extreme events. This study has the aim to evaluate and to quantify synergetic potentials emerging from a combination of current state of the art techniques used to monitor intra-annual wood formation processes. Norway spruce trees were studied in detail during the growing season 2009 with weekly sampling of microcores, high resolution point-dendrometers and wood anatomical analysis. The combination of the applied techniques allowed us to convert the spatial scales of radial tracheid diameter profiles to seasonal time scales and to synchronize fluctuations in intra-annual cell diameter profiles. This spatiotemporal information was used to validate the recently introduced software MICA (Multiple interval-based curve alignment). In comparison to the conventional approach of averaging profiles of tree ring variables, the MICA aligned profiles exhibit a significantly higher synchronicity of the averaged data points. We also demonstrate two new features in the MICA application that enable to extrapolate spatiotemporal information between intra-annual profiles for the construction of robust mean (consensus) profiles that are representative for the population dynamics. By using a set of complementary techniques in an integrated approach, this study highlights a new methodological framework that can contribute to a better understanding of the environmental control of wood formation during the growing season.     

Ensuring a representative sample of earlywood vessels for dendroecological studies: an example from two ring-porous species

The analysis of time series of wood cell anatomical features (such as the earlywood vessels of ring-porous trees) is a successful approach to understand the effect of environmental factors on tree growth and thus constitutes a valuable source of information about past environmental conditions. However, despite the rising interest in analyzing wood anatomical time series, little or no attention has been paid to establish an adequate sample of cells in order to minimize the risk of missing a valuable environmental signal. In order to contribute to such methodological bases, this paper is aimed at (1) identifying a representative sample of earlywood vessels within a tree, which encode the same climatic information, and (2) assessing if it is preferable to obtain the sample of vessels along one or two radii. Four individuals of sessile oak (Quercus petraea (Mattuschka) Liebl.) and sweet chestnut (Castanea sativa Mill.) were harvested and all their earlywood vessel lumina were measured along two 40-mm wide radial strips. Measured vessels were selected stepwise while increasing the tangential width of the wood section from 1 to 40 mm, analyzing at each step (1) the common signal of chronologies and (2) the correlation to the main climatic variables controlling growth. Additionally, both radii in each tree were analyzed together and separately. The results showed that a total tangential width of 10 mm was enough to stabilize the climatic signal with improvement when distributed along two different radii, but a slightly larger tangential width was required to reach an optimal common signal. We suggest that, at least for the case of these two species growing at this specific climatic context, two 5-mm increment cores ensure a representative vessel selection.     

New perspectives for wood anatomical analysis in dendrosciences: The GSL1-microtome

The variability of wood anatomical features in the rings of trees and shrubs is known to be dependent on multifaceted environmental parameters. The ability to determine anatomical variations over longer time periods as decades or centuries is a step forward in dendroecological and dendroclimatological research. In this regard micro sectioning is still one of the basic requirements but sectioning devices (microtomes) designed for wood anatomical purposes are rarely available. We present an affordable heavy duty, but light-weight microtome operated with removable blades. This portable device enables the production of large sections for dendroclimatological reconstructions as well as various types of common sections for wood anatomical studies.     

Preparing micro sections of entire (dry) conifer increment cores for wood anatomical time-series analyses

The type of samples most commonly used in dendro sciences are increment cores of conifers. These cores allow for an easy determination and measurement of ring-width variations over long time periods. For wood anatomical analyses, the cores have to be split into pieces to enable the preparation of high quality micro sections for detailed measurements of cell properties. A major drawback of this procedure is the fact that it is labor intensive and time consuming. We present a new technique enabling the preparation of micro sections of entire increment cores up to a length of 40 cm. For that purpose we combined standard wood-anatomical techniques with the application of Mowiol glue and common Tesa tape. We tested the introduced method on increment cores of Larix decidua Mill. sampled years ago for ring-width analyses to reanalyze them on a microscopic level. The ability to cut these long sections will tremendously reduce the time needed to prepare micro sections. This is of special interest for wood anatomical image analyses of cores used before to create long ring-width chronologies for any kind of environmental reconstructions.     

Coordination of foliar and wood anatomical traits contributes to tropical tree distributions and productivity along the Malay-Thai Peninsula

Drought is a critical factor in plant species distributions. Much research points to its relevance even in moist tropical regions. Recent studies have begun to elucidate mechanisms underlying the distributions of tropical tree species with respect to drought; however, how such desiccation tolerance mechanisms correspond with the coordination of hydraulic and photosynthetic traits in determining species distributions with respect to rainfall seasonality deserves attention. In the present study, we used a common garden approach to quantify inherent differences in wood anatomical and foliar physiological traits in 21 tropical tree species with either widespread (occupying both seasonal and aseasonal climates) or southern (restricted to aseasonal forests) distributions with respect to rainfall seasonality. Use of congeneric species pairs and phylogenetically independent contrast analyses allowed examination of this question in a phylogenetic framework. Widespread species opted for wood traits that provide biomechanical support and prevent xylem cavitation and showed associated reductions in canopy productivity and consequently growth rates compared with southern species. These data support the hypothesis that species having broader distributions with respect to climatic variability will be characterized by traits conducive to abiotic stress tolerance. This study highlights the importance of the well-established performance vs. stress tolerance trade-off as a contributor to species distributions at larger scales.     

Angiosperm wood evolution and the potential contribution of paleontological data

Wood anatomy is often viewed as a source of independent data that may be used to assess evolutionary relationships among angiosperms. Comparative anatomical studies document suites of correlated characters that have been interpreted as general evolutionary trends, of which several have been asserted to be irreversible. Paleobotanical data summarized by Wheeler and Baas provide broad chronological corroboration of some wood anatomical trends, such as evolution from scalariform to simple perforation plates and long to short vessel elements. However, the focus on general evolutionary trends rather than on analyzing character distribution patterns in a cladistic phylogenetic context obscures a more detailed understanding of the evolution of wood anatomical features. Patterns of character evolution, including the assertions of irreversibility, need to be tested through cladistic analyses. In this paper selected wood anatomical features from families of Magnoliidae and “lower” Hamamelididae are summarized and mapped onto previously published cladograms as a preliminary means of testing previous hypotheses of wood evolution. The results show that many of the characters are homoplasious and have evolved both in accord with, and counter to, the hypothesized general trends in different groups of flowering plants. In general, changes that confirm generalized trends are more common than changes that are counter to those trends. Future studies should combine wood anatomical characters with other features as part of a cladistic analysis. Fossil woods have not yet contributed significantly to phylogenetic studies, but in the very few cases where they have been linked to fossil reproductive structures, the woods have provided a better understanding of wood anatomy in early members of some families. Data from fossil wood expand the diversity of anatomical structure known in some angiosperm taxa and thus provide additional evidence that might be used in phylogenetic analyses. Fossil woods have the greatest potential to affect phylogenetic analyses where they can be linked to other fossil organs. The best chance for establishing such a linkage is through the study of fossil charcoalified woods that co-occur with other dispersed mesofossils.     

ROXAS – A new tool to build centuries-long tracheid-lumen chronologies in conifers

Measurements of tree-ring features (ring width, density, isotopes concentration, etc.) are well-established proxies of environmental variability and, in particular, climate fluctuation at local, regional and continental scales. In recent years, tree-ring anatomical structure (conduit size, density, cell wall thickness, ray abundance, etc.) has been recognized as a novel source of valuable ecological information. However, despite the high potential interest, these kinds of investigations have been significantly constrained by the methodological limitations and time-consuming procedures of data collection.In this paper, we present ROXAS: an image analysis tool specifically designed to automatically recognize and measure conduit lumen area and calculate reliable statistics in a reasonable amount of time. With ROXAS, many of the aforementioned limitations in analyzing tree-ring anatomical structure can potentially be overcome. While ROXAS was previously used exclusively for angiosperm analysis, we demonstrate in this paper for the first time how it can also be used to analyze an entire sample of a conifer wood.The use of ROXAS for the analysis of conifer anatomy is exemplified by a 120-year long Pinus leucodermis sample including about 75,000 tracheid cells. The results of ROXAS fully automatic tracheid detection are compared to the results obtained after using in-built manual editing capabilities. While both approaches proved to be efficient, the quality of the fully automatic tracheid detection is found to be generally sufficient for most research applications.     

Introducing anatomical techniques to subfossil wood

Successful cross-dating of subfossil wood, ideally in combination with precise information on germination and dieback, requires the accurate detection of tree-ring width (TRW) boundaries along continuous measurement tracks from pith to bark. However, wood decay and the mechanical deformation of cells often challenge the dendrochronological analysis and subsequent paleoclimatic and environmental interpretations. Here, we show that wood anatomical techniques can improve the assessment of heavily degraded and/or deformed material. We apply state-of-the-art sample preparation, thin sectioning and double-staining to a unique collection of Late Glacial pines that were growing ∼13,000 years ago in the vicinity of Zurich, Switzerland. Highly resolved anatomical observations not only reveal detailed insights into the quality of each cell, but also allow the extent of wood deformation to be identified. By improving the detection and cross-dating of particularly narrow rings, TRW series might be extended towards the pith and bark, where decomposition and distortion is usually most severe, thus adding to a better understanding of possible germination and dieback processes, respectively. Moreover, thin sectioning has the potential to manually reconstruct original TRWs by correcting for post-mortem deformed ring structures. Our results suggest that anatomical techniques should be routinely applied in the assessment of historical, archaeological and subfossil wood.     

A phylogenetic and functional perspective on the origin and evolutionary shifts of growth ring anatomical markers in seed plants

We reconstruct the evolutionary changes in different anatomical markers in order to understand the evolution and functional aspects of growth rings during the diversification of seed plants (spermatophytes), one of the largest and most diverse lineages of the tree of life. We carried out a wide revision of the anatomy of secondary xylem in spermatophytes and reconstructed the evolution of the different anatomical markers in a time-calibrated phylogeny. By embodying a functionally and evolutionarily significant concept in growth rings we reveal a new panorama for their frequency and show how common they are in diverse lineages of tropical plants. In this context, the principal anatomical markers of growth rings are identified in the evolutionary history of plants and their association with climate-related ecological characteristics. We discuss the function of these anatomical markers, especially for thick-walled and/or radially flattened latewood fibres, fibre zone and dilated rays. Despite the high evolutionary lability of the anatomical markers evidenced by our analyses, they appear to represent deep homologies.     

A new Fiji-plugin for visualizing intra-annual density fluctuations and analyzing intra-annual theoretical volumetric flow rate fluctuations along wood cross-sections

Intra-annual analysis of wood samples by examination of xylem structure offers the possibility to reveal structural adaptations in the xylem of trees to varying climatic conditions with a high temporal resolution. Additionally, it can help closing the gap between annual tree ring width measurements and ecophysiological field studies.Typically, two approaches for intra-annual wood analyses are used: densitometry (x-ray or high frequency measurements) and analyses of microscopic images of cross-sections. While densitometry has recently become the most commonly used method, it requires expensive measurement devices, which are not necessarily part of standard laboratory equipment and accordingly not affordable for a significant number of researchers.We therefore present a new plugin for visualizing intra-annual density fluctuations (IADF) and, more specifically, for analyzing the theoretical volumetric flow rate with an adapted Hagen-Poiseuille law for elliptic conduits per pixel-column. The implemented algorithm represents an alternative for intra-annual analysis of microscopic cross-section images. The plugin has been developed for Fiji, a common package based on the open-source image processing program ImageJ to avoid the use of commercial programs for anatomical analyses.     

High-field EPR

Among the numerous spectroscopic techniques utilized in photosynthesis research, high-field/high-frequency EPR and its pulse extensions ESE, ENDOR, ESEEM, and PELDOR play an important role in the endeavor to understand, on the basis of structure and dynamics data, dominant factors that control specificity and efficiency of light-induced electron- and proton-transfer processes in primary photosynthesis. Short-lived transient intermediates of the photocycle can be characterized by high-field EPR techniques, and detailed structural information can be obtained even from disordered sample preparations. The chapter describes how multifrequency high-field EPR methodology, in conjunction with mutation strategies for site-specific isotope or spin labeling and with the support of modern quantum-chemical computation methods for data interpretation, is capable of providing new insights into the photosynthetic transfer processes. The information obtained is complementary to that of protein crystallography, solid-state NMR and laser spectroscopy.     

不同尺度下停歇点湿地对迁徙水鸟的影响研究综述

停歇点湿地是迁徙水鸟重要的能量补给地,在水鸟每年的往返迁徙过程中具有十分重要的生态意义。近年来随着全球变化和人类活动增加,迁飞路线上的停歇点湿地正发生剧烈变化。各个停歇点湿地的生境变化及周围环境不仅是影响水鸟栖息地适宜性的重要因素,还改变了各路线上迁徙水鸟的种群大小和群落多样性。分析不同尺度下停歇点湿地影响迁徙水鸟种群变化的主要生态因子和环境因素,不仅有助于理解各停歇点景观变化的生态效应,也可为迁徙水鸟种群保护提供理论支持。首先分析了在栖息地斑块尺度上停歇点湿地内的水、食物、栖息地格局和人类干扰等生态要素对水鸟觅食和栖息活动的影响;其次,分析了景观尺度上湿地周围的气候变化、土地利用和外来生物等环境条件在各停歇点对水鸟栖息地质量的改变;最后,基于多尺度条件下湿地影响因素的耦合效应,分析了当前湿地生境与水鸟种群关系研究中存在的主要问题,并总结了对湿地和水鸟保护的启示。     

Discrete versus continuous analysis of anatomical and δ13C variability in tree rings with intra-annual density fluctuations

Intra-annual density fluctuations (IADFs) are anomalies of tree rings where wood density is abruptly altered after sudden changes in environmental conditions. Their characterisation can provide information about the relationship between environmental factors and eco-physiological processes during tree growth. This paper reports about the variability of anatomical traits and stable carbon isotopic composition along tree rings as resulting from the application of two different methodological approaches: (a) the separation of each ring into different regions (earlywood, latewood and IADF) and the comparison of anatomical and isotopic parameters measured in those specific sectors and (b) the analysis of such features in continuum along ring width. Moreover, different parameters of vessels (i.e. ecd—equivalent circle diameter, elongation, sphericity and convexity of vessel lumen) were considered to identify those more appropriate for the representation of intra-annual anatomical variations. The analysis was conducted on Arbutus unedo L. growing on the Elba Island (Italy); tree rings of this species form IADFs with features clearly responsive to the environmental conditions experienced during plant growth. Results showed that the first approach, although more suitable to obtain data for subsequent statistical comparisons and for the calculation of correlations with environmental parameters, suffers from elements of subjectivity due to the size and position of the selected tree-ring regions. The in continuum method allows a clearer identification of the variation of tree-ring properties along ring width. Regarding anatomical parameters, shape indexes were not suitable indicators of intra-annual variability. The overall analysis suggested that using both methodologies in synergy helps to gain complete information and avoid misleading interpretations of IADFs in tree rings.     

Temporal annotation of high-resolution intra-annual wood density information of Eucalyptus urophylla and its correlation with hydroclimatic conditions

Three different Eucalyptus urophylla clones grown under two different spacing regimes in an experimental site in the state of São Paulo, Brazil, were analyzed to test effects of clone identity, spacing, cambial age and hydroclimatic conditions on high-resolution intra-annual wood density profiles. Since distinct periodic tree-ring boundaries were not visible on the stem cross-sectional surfaces, finding an alternative method for synchronization of density profiles was crucial for the analysis. The challenge was to generate intra- and inter-tree synchronized density profiles that possess high amplitude variation and low phase variation. Thus, we developed a protocol and workflow of how such high-resolution density profiles can be spatially aligned and temporally annotated to enable correlation analyses between trees and with time series of environmental stimuli. Mean wood density was significantly different between clones, but not between the spacings. Wood density increased significantly with increasing cambial age and decreasing growth rate. Principal component analysis showed that the overall variability in the temporally annotated density profiles is dominated by a highly significant common signal. We found significant negative correlation values for precipitation, indicating that water supply is the main driver of stem growth at the site, and providing evidence for the correctness of the method. The developed workflow can easily be adjusted to the analysis of other intra-annual tree-ring features like anatomical xylem cell traits or isotopic signals in the wood. It has a large potential to be used as a general guideline for the synchronization of intra-annual tree-ring traits, especially when distinct tree-ring boundaries are missing, as it is often the case under tropical climatic conditions. The workflow supports the development of spatially aligned and temporally annotated chronologies under non-annual growth rhythms.     

CAMBIUM, a process-based model of daily xylem development in Eucalyptus

In hardwoods such as Eucalyptus spp., xylem (wood) is a heterogeneous tissue consisting of multiple cell types. As such, xylem development involves multiple complex interactions. To describe and understand xylem development, and ultimately predict the resultant wood properties, a process-based approach to modelling wood property variation is potentially very useful. In this paper, a new model (CAMBIUM), which incorporates concepts of these processes, is described. CAMBIUM predicts how wood density and fibre and vessel anatomical properties vary from pith-to-bark at a daily time step as a function of changing environmental conditions and a set of simulated physiological processes. Simulations from an existing process-based model of stand development (CABALA) are used as inputs. A key feature of CAMBIUM is a model of the interaction between different xylem cell types. Some weaknesses were identified in the ability of the model to simulate vessel spatial patterns and frequencies, emphasizing the complexities inherent in this aspect of angiosperm wood formation. The model was, however, able to provide realistic estimates of short-term variation and temporal ranges in eucalypt fibre diameter and secondary wall development and wood density.     

Inferring Latent States and Refining Force Estimates via Hierarchical Dirichlet Process Modeling in Single Particle Tracking Experiments

Understanding the basis for intracellular motion is critical as the field moves toward a deeper understanding of the relation between Brownian forces, molecular crowding, and anisotropic (or isotropic) energetic forcing. Effective forces and other parameters used to summarize molecular motion change over time in live cells due to latent state changes, e.g., changes induced by dynamic micro-environments, photobleaching, and other heterogeneity inherent in biological processes. This study discusses limitations in currently popular analysis methods (e.g., mean square displacement-based analyses) and how new techniques can be used to systematically analyze Single Particle Tracking (SPT) data experiencing abrupt state changes in time or space. The approach is to track GFP tagged chromatids in metaphase in live yeast cells and quantitatively probe the effective forces resulting from dynamic interactions that reflect the sum of a number of physical phenomena. State changes can be induced by various sources including: microtubule dynamics exerting force through the centromere, thermal polymer fluctuations, and DNA-based molecular machines including polymerases and protein exchange complexes such as chaperones and chromatin remodeling complexes. Simulations aiming to show the relevance of the approach to more general SPT data analyses are also studied. Refined force estimates are obtained by adopting and modifying a nonparametric Bayesian modeling technique, the Hierarchical Dirichlet Process Switching Linear Dynamical System (HDP-SLDS), for SPT applications. The HDP-SLDS method shows promise in systematically identifying dynamical regime changes induced by unobserved state changes when the number of underlying states is unknown in advance (a common problem in SPT applications). We expand on the relevance of the HDP-SLDS approach, review the relevant background of Hierarchical Dirichlet Processes, show how to map discrete time HDP-SLDS models to classic SPT models, and discuss limitations of the approach. In addition, we demonstrate new computational techniques for tuning hyperparameters and for checking the statistical consistency of model assumptions directly against individual experimental trajectories; the techniques circumvent the need for “ground-truth” and/or subjective information.     

A short review of model selection techniques for radiation epidemiology

A common type of statistical challenge, widespread across many areas of research, involves the selection of a preferred model to describe the main features and trends in a particular data set. The objective of model selection is to balance the quality of fit to data against the complexity and predictive ability of the model achieving that fit. Several model selection techniques, including two information criteria, which aim to determine which set of model parameters the data best support, are reviewed here. The techniques rely on computing the probabilities of the different models, given the data, rather than considering the allowed values of the fitted parameters. Such information criteria have only been applied to the field of radiation epidemiology recently, even though they have longer traditions of application in other areas of research. The purpose of this review is to make two information criteria more accessible by fully detailing how to calculate them in a practical way and how to interpret the resulting values. This aim is supported with the aid of some examples involving the computation of risk models for radiation-induced solid cancer mortality fitted to the epidemiological data from the Japanese A-bomb survivors. These examples illustrate that the Bayesian information criterion is particularly useful in concluding that the weight of evidence is in favour of excess relative risk models that depend on age-at-exposure and excess relative risk models that depend on age-attained.     

Growth-ring boundaries of tropical tree species: Aiding delimitation by long histological sections and wood density profiles

Recent methodological advances have opened new perspectives for tropical dendrochonological studies by facilitating the visualization, delimitation, and analyses of tree-rings. One of those improvements was brought by X-ray densitometry, which allows building radial wood density profiles at microscopic scale. Furthermore, recent methods allow for cutting long histological sections to study anatomical variations along the entire radius of trees. These techniques have mainly been applied to low wood-density species from temperate and Mediterranean regions, with only limited applications in the tropics. Here we provide an improved protocol that allows for obtaining long histological sections of tropical woods, apply it to six species with varying wood densities 0.45−0.85 g cm⁻³ (Eucalyptus grandis, Tectona grandis, Acacia mangium, Cedrela fissilis, Hymenaea courbaril, and Copaifera duckei), and explore potential applications for tree-ring analyses. We provide instructions on core-microtome knife adjustments, procedures for softening and sectioning long histological samples of high wood-density species. We also present a multi-proxy approach that combines X-ray density profiles with the histological sections that improve the characterization and distinction of the various and complex tropical growth rings anatomical markers (fibre zone, marginal parenchyma, and ring porosity). This multi-proxy approach also opens the door for obtaining quantitative anatomy and physical parameters of tropical species with (intra-annual resolution. Our proposed approach is thus not only an additional tool to improve ring-boundary delimitation of tropical species, but it also paves the way to more innovative, borderline approaches in tropical dendrochronology.     

Effects of flooding on wood and bark anatomy of four species in a mangrove forest community

Variation in the wood and bark anatomy of the dominant species of a mangrove forest community in Mexico was evaluated in relation to some environmental factors, and their physiological adaptations to salinity and flooding period are discussed. The forest is characterized by three zones according to the presence of dominant tree species and flooding periodicity. Vessel arrangement and wood and bark ray height are strongly associated with flooding zones where trees are growing. Variance analyses revealed significant differences among zones for these anatomical characteristics. Soil texture and water salinity were the most useful parameters for the prediction of values of anatomical characteristics. More abundant vessels in radial multiples in a shorter flooding period suggest a functional advantage of multiple vessel groups. Taller wood and bark rays in response to prolonged flooding period can be attributed to anoxic conditions. Among zones, significant differences in the vulnerability index of the species were detected, but not with respect to relative conductivity. Significant differences among zones exist for wood and bark characteristics involved in vertical and horizontal water transport, photosynthates and gas exchange.     

Arbuscular mycorrhizas and biological control of soil-borne plant pathogens – an overview of the mechanisms involved

 Biological control of plant pathogens is currently accepted as a key practice in sustainable agriculture because it is based on the management of a natural resource, i.e. certain rhizosphere organisms, common components of ecosystems, known to develop antagonistic activities against harmful organisms (bacteria, fungi, nematodes etc.). Arbuscular mycorrhizal (AM) associations have been shown to reduce damage caused by soil-borne plant pathogens. Although few AM isolates have been tested in this regard, some appear to be more effective than others. Furthermore, the degree of protection varies with the pathogen involved and can be modified by soil and other environmental conditions. This prophylactic ability of AM fungi could be exploited in cooperation with other rhizospheric microbial angatonists to improve plant growth and health. Despite past achievements on the application of AM in plant protection, further research is needed for a better understanding of both the ecophysiological parameters contributing to effectiveness and of the mechanisms involved. Although the improvement of plant nutrition, compensation for pathogen damage, and competition for photosynthates or colonization/infection sites have been claimed to play a protective role in the AM symbiosis, information is scarce, fragmentary or even controversial, particularly concerning other mechanisms. Such mechanisms include (a) anatomical or morphological AM-induced changes in the root system, (b) microbial changes in rhizosphere populations of AM plants, and (c) local elicitation of plant defence mechanisms by AM fungi. Although compounds typically involved in plant defence reactions are elicited by AM only in low amounts, they could act locally or transiently by making the root more prone to react against pathogens. Current research based on molecular, immunological and histochemical techniques is providing new insights into these mechanisms. Accepted: 29 October 1996