Synchrotron-based techniques for plant and soil science: opportunities, challenges and future perspectives

Spectroscopic approaches to plant and soil sciences have provided important information for several decades. However, many of these approaches suffered from a number of limitations and drawbacks especially in terms of spatial resolution and requirements for sample preparation. The advent of dedicated synchrotron facilities, that allow the exploitation of the particular qualities of synchrotron radiation as a research tool, has revolutionised the way we approach the investigation of nutrients and contaminants in environmental samples. Various synchrotron-based techniques are currently available that permit such investigations in situ and at the molecular level. The continuous development of these techniques is delivering substantial gains in terms of sensitivity and spatial resolution which allows analyses of diluted samples at the sub-micron scale. This paper aims at providing an introduction to synchrotron radiation and to the fundamentals of some widely used synchrotron-based techniques, in particular X-ray absorption, fluorescence and tomography. Furthermore, examples are provided regarding the applications of synchrotron-based techniques in the field of plant, soil and rhizosphere research. Finally, current limitations and future perspectives of synchrotron techniques are discussed.     

Spatial variability of the soil seed bank in a heterogeneous ephemeral wetland system in semi-arid Australia

Soil seed banks are an important component of plant community diversity in ephemeral wetlands, allowing many species to persist through unpredictable periods of flood and drought. Spatial variation of extant vegetation in such habitats commonly reflects patterns of flood history and often varies predictably between broadly differing hydro-geomorphic habitat types. Here we investigate whether spatial variation of soil seed banks is similarly controlled by fluvial processes at this scale. Results are presented from a seedling emergence trial using samples collected from a range of habitat types, and at different scales within these, in the ephemeral Narran Lakes system in semi-arid Australia. Composition and structure of soil seed banks varied significantly between habitat types reflecting broad differences in flood frequency. As predicted, germinable seed abundance was found to be highest in intermediately flooded habitats. Variability in soil seed bank composition at a local scale was also found to be influenced by hydrology with greater spatial heterogeneity evident in the river channel as well as amongst the least frequently inundated riparian and floodplain habitats.     

Comparison of three seed trap types in a chalk grassland: toward a standardised protocol

In a chalk grassland in north-western France, vegetation and seed rain were studied along two transects. We compared the efficiency of three types of seed traps (funnel traps, sticky traps, pots exposed in the field) to estimate the annual seed rain and to reveal various processes involved in plant community regeneration. Data were analysed to compare seed density, species richness and composition across seed traps and vegetation. Geostatistical analyses (semivariograms. were used to detect possible autocorrelation and to examine patterns of spatial variation in seed rain and vegetation. The results show that (1) funnel traps are most efficient (56 species, 8079 seeds.m^–2). (2) Each type of seed traps brings different information about the processes involved in seed dispersal and seedling establishment. Sticky traps help to understand import and export of seeds in a community through anemochory. Funnel traps may provide a measure of the auto-regeneration capacity of the vegetation through its local seed production. Pot traps integrate various processes involved between seed dispersal and seedling emergence. (3.) The exposition to environmental conditions generates marked spatial patterns in species richness measured in pots and in vegetation, selecting species able to survive. Pot traps indicate that numerous species producing seeds in standing vegetation are unable to establish in the field through seedling recruitment. Our study emphasizes the need of using different types of seed traps and spatial sampling configurations to assess the regenerative potential of standing vegetation and the various mechanisms involved in seed dispersal. A standardised protocol for seed rain sampling was finally developed.     

Are local plants the best for ecosystem restoration? It depends on how you analyze the data

One of the key questions in ecosystem restoration is the choice of the seed material for restoring plant communities. The most common strategy is to use local seed sources, based on the argument that many plants are locally adapted and thus local seed sources should provide the best restoration success. However, the evidence for local adaptation is inconsistent, and some of these inconsistencies may be due to different experimental approaches that have been used to test for local adaptation. We illustrate how conclusions about local adaptation depend on the experimental design and in particular on the method of data analysis. We used data from a multispecies reciprocal transplant experiment and analyzed them in three different ways: (1) comparing local vs. foreign plants within species and sites, corresponding to tests of the “local is best” paradigm in ecological restoration, (2) comparing sympatric vs. allopatric populations across sites but within species, and (3) comparing sympatric and allopatric populations across multiple species. These approaches reflect different experimental designs: While a local vs. foreign comparison can be done even in small experiments with a single species and site, the other two approaches require a reciprocal transplant experiment with one or multiple species, respectively. The three different analyses led to contrasting results. While the local/foreign approach indicated lack of local adaptation or even maladaptation, the more general sympatric/allopatric approach rather suggested local adaptation, and the most general cross‐species sympatric/allopatric test provided significant evidence for local adaptation. The analyses demonstrate how the design of experiments and methods of data analysis impact conclusions on the presence or absence of local adaptation. While small‐scale, single‐species experiments may be useful for identifying the appropriate seed material for a specific restoration project, general patterns can only be detected in reciprocal transplant experiments with multiple species and sites.     

Topographic and Bioclimatic Determinants of the Occurrence of Forest and Grassland in Tropical Montane Forest-Grassland Mosaics of the Western Ghats,India

The objective of this analysis was to identify topographic and bioclimatic factors that predict occurrence of forest and grassland patches within tropical montane forest-grassland mosaics. We further investigated whether interactions between topography and bioclimate are important in determining vegetation pattern, and assessed the role of spatial scale in determining the relative importance of specific topographic features. Finally, we assessed the role of elevation in determining the relative importance of diverse explanatory factors. The study area consists of the central and southern regions of the Western Ghats of Southern India, a global biodiversity hotspot. Random forests were used to assess prediction accuracy and predictor importance. Conditional inference classification trees were used to interpret predictor effects and examine potential interactions between predictors. GLMs were used to confirm predictor importance and assess the strength of interaction terms. Overall, topographic and bioclimatic predictors classified vegetation pattern with approximately 70% accuracy. Prediction accuracy was higher for grassland than forest, and for mosaics at higher elevations. Elevation was the most important predictor, with mosaics above 2000m dominated largely by grassland. Relative topographic position measured at a local scale (within a 300m neighbourhood) was another important predictor of vegetation pattern. In high elevation mosaics, northness and concave land surface curvature were important predictors of forest occurrence. Important bioclimatic predictors were: dry quarter precipitation, annual temperature range and the interaction between the two. The results indicate complex interactions between topography and bioclimate and among topographic variables. Elevation and topography have a strong influence on vegetation pattern in these mosaics. There were marked regional differences in the roles of various topographic and bioclimatic predictors across the range of study mosaics, indicating that the same pattern of grass and forest seems to be generated by different sets of mechanisms across the region, depending on spatial scale and elevation.     

Inflorescences: concepts,function, development and evolution

Background

Inflorescences are complex structures with many functions. At anthesis they present the flowers in ways that allow for the transfer of pollen and optimization of the plant''s reproductive success. During flower and fruit development they provide nutrients to the developing flowers and fruits. At fruit maturity they support the fruits prior to dispersal, and facilitate effective fruit and seed dispersal. From a structural point of view, inflorescences have played important roles in systematic and phylogenetic studies. As functional units they facilitate reproduction, and are largely shaped by natural selection.

Scope

The papers in this Special Issue bridge the gap between structural and functional approaches to inflorescence evolution. They include a literature review of inflorescence function, an experimental study of inflorescences as essential contributors to the display of flowers, and two papers that present new methods and concepts for understanding inflorescence diversity and for dealing with terminological problems. The transient model of inflorescence development is evaluated in an ontogenetic study, and partially supported. Four papers present morphological and ontogenetic studies of inflorescence development in monophyletic groups, and two of these evaluate the usefulness of Hofmeister''s Rule and inhibitory fields to predict inflorescence structure. In the final two papers, Bayesian and Monte-Carlo methods are used to elucidate inflorescence evolution in the Panicoid grasses, and a candidate gene approach is used in an attempt to understand the evolutionary genetics of inflorescence evolution in the genus Cornus (Cornaceae). Taken as a whole, the papers in this issue provide a glimpse of contemporary approaches to the study of the structure, development, and evolution of inflorescences, and suggest fruitful new directions for research.     

Imaging techniques for assaying lymphocyte activation in action

Imaging techniques have greatly improved our understanding of lymphocyte activation. Technical advances in spatial and temporal resolution and new labelling tools have enabled researchers to directly observe the activation process. Consequently, research using imaging approaches to study lymphocyte activation has expanded, providing an unprecedented level of cellular and molecular detail in the field. As a result, certain models of lymphocyte activation have been verified, others have been revised and yet others have been replaced with new concepts. In this article, we review the current imaging techniques that are used to assess lymphocyte activation in different contexts, from whole animals to single molecules, and discuss the advantages and potential limitations of these methods.     

Model collaboration for the improved assessment of biomass supply,demand, and impacts

Existing assessments of biomass supply and demand and their impacts face various types of limitations and uncertainties, partly due to the type of tools and methods applied (e.g., partial representation of sectors, lack of geographical details, and aggregated representation of technologies involved). Improved collaboration between existing modeling approaches may provide new, more comprehensive insights, especially into issues that involve multiple economic sectors, different temporal and spatial scales, or various impact categories. Model collaboration consists of aligning and harmonizing input data and scenarios, model comparison and/or model linkage. Improved collaboration between existing modeling approaches can help assess (i) the causes of differences and similarities in model output, which is important for interpreting the results for policy‐making and (ii) the linkages, feedbacks, and trade‐offs between different systems and impacts (e.g., economic and natural), which is key to a more comprehensive understanding of the impacts of biomass supply and demand. But, full consistency or integration in assumptions, structure, solution algorithms, dynamics and feedbacks can be difficult to achieve. And, if it is done, it frequently implies a trade‐off in terms of resolution (spatial, temporal, and structural) and/or computation. Three key research areas are selected to illustrate how model collaboration can provide additional ways for tackling some of the shortcomings and uncertainties in the assessment of biomass supply and demand and their impacts. These research areas are livestock production, agricultural residues, and greenhouse gas emissions from land‐use change. Describing how model collaboration might look like in these examples, we show how improved model collaboration can strengthen our ability to project biomass supply, demand, and impacts. This in turn can aid in improving the information for policy‐makers and in taking better‐informed decisions.     

生物土壤结皮对种子萌发和幼苗建植的影响研究进展

生物土壤结皮（BSC）在陆地生态系统中具有重要的生态地位,尤其是旱地生态系统中,BSC占据了种子植物之间的广阔地面。因此,BSC的发展必然影响种子植物更新过程与植被空间格局;但其作用方式、影响程度等因相关研究涉及多气候要素、土壤类型、BSC组成物种和种子植物物种的差异及其不同组合,导致目前的研究结论存在广泛争议。研究综合论述了BSC改变地表微形态对种子传播过程的影响;BSC改变土壤特性（物理、化学、生物学）对种子萌发和幼苗存活与建植等关键环节的影响;并结合种子形态特征及种子萌发、幼苗建植的性状等,综合分析了BSC对种子传播、种子萌发与幼苗建植等更新过程的潜在影响机理;探讨了目前研究矛盾性结论产生的原因。总体来说,深入研究并全面揭示BSC对种子植物更新过程的影响,应加强学科交叉,将分子生物学、植物生理学、生物化学等微观研究,与遥感、野外生态因子过程监测、控制实验等宏观、中观研究结合,从机理到过程方面动态研究BSC对种子植物更新过程的影响,并引入水文模型、气候模型、种群动态模型等模型预测方法,研究气候变化、各类干扰频发的情景下,BSC对种子传播、萌发及幼苗建植过程的潜在影响,以期促进对BSC与种子植物间相互关系的研究,加深对干旱脆弱生态系统植被发展规律的认识。     

Effect of spatial and temporal heterogeneity on granivory in the Monte Desert,Argentina

Abstract An important aspect of arid regions is the spatial heterogeneity resulting from differences among plant communities. There are process differences among different vegetation patches increasing variability in the functioning of the ecosystem. The purpose of this study was to estimate granivory, by studying variation of seed removal rates among patches at the local scale and variation according to seed type. We carried out experiments during four seasons in three plant communities in the Monte Desert, Argentina: ‘peladal’, mesquite forest and creosotebush. Seed trays were offered to ants, birds and rodents. Two types of commercial seeds (sunflower and millet) were used. We found that seed removal rate was significantly different among plant communities, among taxa (birds, ants and murid rodents), and among seasons, and that removal rate was higher for sunflower. Seed removal rates by murid rodents were higher than by birds or ants, and occasionally as high as those found in other deserts. The heterogeneity of seed removal patterns at the local level was as strong as that found between continents. Further studies may show similar local heterogeneity in other deserts of the world.     

Plant functional types and disturbance dynamics – Introduction

Abstract. Plant functional traits and types are useful concepts in relation to disturbance responses of natural and managed ecosystems. To explore their applicability in greater depth, a set of 12 papers presents a broad range of issues from methodologies to the results of particular trait studies in the field, and modelling approaches. So far, empirical studies have only allowed us to identify a few functional traits that are consistently associated with disturbance. To determine the trait variations associated with climate, disturbance history and current disturbance regime as well as the interactions between these factors, global-scale comparisons of numerous individual studies are required. Significant advances toward this ambitious goal are presented in these papers, and include: (1) the articulation of experimental and analytical methodologies for individual studies that could usefully contribute to a global comparison; (2) the identification of core traits that can be used in the further search for disturbance-related traits common to a range of environments; (3) further information on vegetation response to disturbance in terms of trait representation, and the identification of attribute syndromes; (4) the identification of issues for modelling disturbance dynamics using functional types.     

Seedling emergence responds to both seed source and recruitment site climates: a climate change experiment combining transplant and gradient approaches

Seedling recruitment allows genetic recombination and production of dispersal units. Both the climate experienced by the source populations (seed source effect) and the weather experienced by the seeds during germination and seedling emergence (recruitment site effects) are important for seedling recruitment. Separating these effects in the field is essential to assess potential climate change impacts on plant population. We combine experimental seed transplant and gradient analyses to separate the effects of seed source and recruitment site temperature and precipitation for the seedling emergence of two alpine/lowland species pairs (Viola biflora/Viola palustris, Veronica alpina/Veronica officinalis). Combining these approaches allows us to compare local responses versus responses along environmental gradients, but also tests for local adaptation and/or pre-conditioning effects (adaptive seedling emergence responses). Veronica officinalis emergence increased with increasing seed source temperature in both the experimental and the gradient approaches, and showed adaptive seedling emergence. Viola biflora, Viola palustris and Veronica alpina emergence decreased with recruitment site temperature in both approaches. Both Violas emergences increased with recruitment site precipitation, in both approaches for the alpine violet, and in the gradient approach for lowland one. Emergence was primarily affected by the environment of the recruitment site, whereas seed source climate and adaptive seedling emergence impacted recruitment in only one of our species. The responses to recruitment site temperatures were negative, whereas the response to seed source temperature was positive. Ignoring the distinctions between these different mechanisms can lead to erroneous conclusions regarding potential climate change impacts on plant recruitment.     

Lights,cytoskeleton, action: Optogenetic control of cell dynamics

Cell biology is moving from observing molecules to controlling them in real time, a critical step towards a mechanistic understanding of how cells work. Initially developed from light-gated ion channels to control neuron activity, optogenetics now describes any genetically encoded protein system designed to accomplish specific light-mediated tasks. Recent photosensitive switches use many ingenious designs that bring spatial and temporal control within reach for almost any protein or pathway of interest. This next generation optogenetics includes light-controlled protein–protein interactions and shape-shifting photosensors, which in combination with live microscopy enable acute modulation and analysis of dynamic protein functions in living cells. We provide a brief overview of various types of optogenetic switches. We then discuss how diverse approaches have been used to control cytoskeleton dynamics with light through Rho GTPase signaling, microtubule and actin assembly, mitotic spindle positioning and intracellular transport and highlight advantages and limitations of different experimental strategies.     

Patterns of resource tracking by avian frugivores at multiple spatial scales: two case studies on discordance among scales

Scaling is relevant for the analysis of plant‐frugivore interaction, since the ecological and evolutionary outcomes of seed dispersal depend on the spatial and temporal scale at which frugivory patterns emerge. We analyse the relationship between fruit abundance and frugivore activity at local and landscape spatial scales in two different systems composed, respectively, by the bird‐dispersed woody plants Juniperus communis and Bursera fagaroides, and their frugivore assemblages. We use a hierarchical approach of nested patchiness of fruit‐resource, where patches are defined by individual plants within site, at the local scale, and by sites within region, at the landscape scale. The structure of patches is also described in terms of contrast (differences in fruit availability among patches) and aggregation (spatial distribution of patches). For J. communis, frugivore activity was positively related to fruit availability at the landscape scale, this pattern seldom emerging at the local scale; conversely, B. fagaroides showed a general trend of positive local pattern that disappeared at the landscape scale. These particular trends might be partially explained by differences in contrast and aggregation. The strong contrast among plants within site together with a high aggregation among sites would promote the B. fagaroides pattern to be only local, whereas in J. communis, low aggregation among sites within region would favour a sharp landscape‐scale pattern. Both systems showed discordant patterns of fruit‐resource tracking among consecutive spatial scales, but the sense of discordance differed among systems. These results, and the available multi‐scale frugivory data, suggest that discordance among successive scales allows to link directly frugivory patterns to resource‐tracking mechanisms acting at particular scales, resulting, thus, more informative than concordance observational data, in which landscape patterns might result from accumulated effect of local mechanisms. In this context, we propose new methodological approaches for a better understanding of the hierarchical behavioural mechanisms underpinning the multi‐scale resource tracking by frugivores.     

Linking seed dispersal and genetic structure of trees: a biogeographical approach

Aim Natural and human‐induced differences in frugivore assemblages can influence the seed dispersal distances of trees. An important issue in seed dispersal systems is to understand whether differences in seed dispersal distances also affect the genetic structure of mature trees. One possible approach to test for a relationship between seed dispersal and the genetic structure of mature trees is to compare the genetic structure of two closely related tree species between two biogeographical regions that differ in frugivore assemblages and seed dispersal distances. Previous studies on two Commiphora species revealed that Commiphora guillauminii in Madagascar has a much lower seed dispersal distance than Commiphora harveyi in South Africa. We tested whether the lower seed dispersal distance might have caused decreased gene flow, resulting in a stronger genetic structure in Madagascar than in South Africa. Location Madagascar and South Africa. Methods Using amplified fragment length polymorphism markers we investigated the genetic structure of 134 trees in Madagascar and 158 trees in South Africa at a local and a regional spatial scale. Results In concordance with our hypothesis, kinship analysis suggests that gene flow was restricted mostly to 3 km in Madagascar and to 30 km in South Africa. At the local spatial scale, the genetic differentiation among groups of trees within sample sites was marginally significantly higher in Madagascar (F_ST = 0.069) than in South Africa (F_ST = 0.021). However, at a regional spatial scale genetic differentiation was lower in Madagascar (F_ST = 0.053) than in South Africa (F_ST = 0.163). Main conclusions Our results show that lower seed dispersal distances of trees were linked to higher genetic differentiation of trees only at a local spatial scale. This suggests that seed dispersal affects the genetic population structure of trees at a local, but not at a regional, spatial scale.     

Establishing Causality between Environmental Stressors and Effects on Aquatic Ecosystems

Establishing causal relationships between environmental stressors and observed effects in natural systems is difficult due to the many intrinsic environmental factors that can hinder this process and because there are no widely accepted and proven approaches for determining such relationships. Several types of approaches or combinations of approaches, each with their own sets of advantages and limitations, have been applied in a variety of ecological systems to investigate possible causal relationships between stressors and effects. These include controlled laboratory studies (including acute and chronic bioassays), experimental field manipulations, field studies based on synoptic field surveys, mathematical simulation modeling, statistical associations, various combinations of laboratory, experimental, and field studies, and the ecoepidemiological (weight or evidence) approach. The use of ecoepidemiological (“forensic toxicology”) principles is becoming increasingly attractive as a method to help establish causality because it does not involve the same limitations of other approaches and it can also be used to integrate disparate information within a logical framework so that scientifically and defensible regulatory decisions can be made. The objective of this Commentary series of papers on the issue on causality is to demonstrate the application of the ecoepidemiology approach, using a variety of case history studies, for establishing causal relationships between specific stressors and biological effects. For each case history provided in the following series of papers, the authors describe their study situation, summarize the results supporting a causal relationship, and then compare their study results against seven standard causal criteria.     

Slow Recovery from Local Disturbances as an Indicator for Loss of Ecosystem Resilience

A range of indicators have been proposed for identifying the elevated risk of critical transitions in ecosystems. Most indicators are based on the idea that critical slowing down can be inferred from changes in statistical properties of natural fluctuations and spatial patterns. However, identifying these signals in nature has remained challenging. An alternative approach is to infer changes in resilience from differences in standardized experimental perturbations. However, system-wide experimental perturbations are rarely feasible. Here we evaluate the potential to infer the risk of large-scale systemic transitions from local experimental or natural perturbations. We use models of spatially explicit landscapes to illustrate how recovery rates upon small-scale perturbations decrease as an ecosystem approaches a tipping point for a large-scale collapse. We show that the recovery trajectory depends on: (1) the resilience of the ecosystem at large scale, (2) the dispersal rate of organisms, and (3) the scale of the perturbation. In addition, we show that recovery of natural disturbances in a heterogeneous environment can potentially function as an indicator of resilience of a large-scale ecosystem. Our analyses reveal fundamental differences between large-scale weak and local-scale strong perturbations, leading to an overview of opportunities and limitations of the use of local disturbance-recovery experiments.     

生态学中的尺度问题——尺度上推

尺度推绎是生态学理论和应用的核心。如何在一个异质景观中进行尺度推绎仍然是一个悬而未决的科学难题,是对当今生态学家在全球变化背景下研究环境问题的重大挑战。就目前的研究,一般可分为四大类尺度推绎途径:空间分析法(如分维分析法和小波分析法)、基于相似性的尺度上推方法、基于局域动态模型的尺度上推方法、随机(模型)法。基于相似性的尺度上推方法来源于生物学上的异量关联,可将其思想延伸至空间上,研究物种丰富度、自然河网、地形特征、生态学格局或过程变量和景观指数等。基于局域动态模型的尺度上推方法需要首先确定是否进行跨尺度推绎,以及是否考虑空间单元之间的水平相互作用和反馈,然后再应用具体的方法或途径,如简单聚合法、有效值外推法、直接外推法、期望值外推、显式积分法和空间相互作用模拟法等。随机(模型)法以其它尺度上推方法为基础,根据研究的是单个景观,还是多个景观,采用不同的途径。理解、定量和降低尺度推绎结果的不确定性已经变得越来越重要,但相关研究仍然极少。以上所有有关尺度推绎的方法、途径和结果分析共同构成了尺度推绎的概念框架。     

A critique of 'countryside biogeography' as a guide to research in human‐dominated landscapes

Proliferation of redundant terms in ecology and conservation slows progress and creates confusion. ‘Countryside biogeography’ has been promoted as a new framework for conservation in production landscapes, so may offer a replacement for other concepts used by landscape ecologists. We conducted a systematic review to assess whether the 'countryside biogeography' concept provides a distinctive framing for conservation in human‐dominated landscapes relative to existing concepts. We reviewed 147 papers referring to countryside biogeography and 81 papers that did not. These papers were divided into categories representing three levels of use of countryside biogeography concepts (strong, weak, cited only) and two categories that did not use countryside biogeography at all but used similar concepts including fragmentation and matrix. We revealed few distinctions among groups of papers. Countryside biogeography papers made more frequent use of the terms 'ecosystem services', 'intensification' and 'land sparing' compared with non‐countryside biogeography papers. Papers that did not refer to countryside biogeography sampled production areas (e.g. farms) less often, and this related to their focus on habitat specialist species for which patch‐matrix assumptions were reasonable. Countryside biogeography offers a conceptual wrapper rather than a distinctive framework for advancing research in human‐modified landscapes. This and similar wrappers such as ‘conservation biogeography’ and ‘agricultural biogeography’ risk creating confusion among new researchers, and can prevent clear communication about research. To improve communication, we recommend using the suite of well‐established terms already applied to conservation in human‐modified landscapes rather than through an interceding conceptual wrapper.