Background

Climate change represents a grand challenge for agricultural productivity. Understanding complex plant traits such as stress tolerance, disease resistance or crop yield is thus essential for breeding and the development of sustainable agriculture strategies. When screening for the most robust plant phenotypes, fast, high-throughput phenotyping represents the means of choice.

Results

We have developed a plant phenotyping platform to measure the emission of volatile organic compounds (VOCs), photosynthetic gas exchange and transpiration under ambient, or abiotic and biotic stress conditions. These parameters are highly suitable markers to non-invasively and dynamically study plant growth and plant stress status, making them perfect test variables for long-term, online plant monitoring. Here we introduce the new phenotyping platform, termed VOC-SCREEN, and present results of a first case study with three barley cultivars, demonstrating that the plant’s volatilome can be successfully applied to discriminate different barley varieties.

Conclusion

Volatilomics is a promising technique to non-invasively screen for plant phenotypic traits.

Context

Despite decades of research, there is an intense debate about the consistency of the hump-shaped pattern describing the relationship between diversity and disturbance as predicted by the intermediate disturbance hypothesis (IDH). Previous meta-analyses have not explicitly considered interactive effects of disturbance frequency and intensity of disturbance on plant species diversity in terrestrial landscapes.

Objective

We conducted meta-analyses to test the applicability of IDH by simultaneously examining the relationship between species richness, disturbance frequency (quantified as time since last disturbance as originally proposed) and intensity of disturbance in forest landscapes.

Methods

The effects of disturbance frequency, intensity, and their interaction on species richness was evaluated using a mixed-effects model.

Results

We found that species richness peaks at intermediate frequency after both high and intermediate disturbance intensities, but the richness-frequency relationship differed between intensity classes.

Conclusions

Our study highlights the need to measure multiple disturbance components that could help reconcile conflicting empirical results on the effect of disturbance on plant species diversity.

Context

Routine movements of large herbivores, often considered as ecosystem engineers, impact key ecological processes. Functional landscape connectivity for such species influences the spatial distribution of associated ecological services and disservices.

Objectives

We studied how spatio-temporal variation in the risk-resource trade-off, generated by fluctuations in human activities and environmental conditions, influences the routine movements of roe deer across a heterogeneous landscape, generating shifts in functional connectivity at daily and seasonal time scales.

Methods

We used GPS locations of 172 adult roe deer and step selection functions to infer landscape connectivity. In particular, we assessed the influence of six habitat features on fine scale movements across four biological seasons and three daily periods, based on variations in the risk-resource trade-off.

Results

The influence of habitat features on roe deer movements was strongly dependent on proximity to refuge habitat, i.e. woodlands. Roe deer confined their movements to safe habitats during daytime and during the hunting season, when human activity is high. However, they exploited exposed open habitats more freely during night-time. Consequently, we observed marked temporal shifts in landscape connectivity, which was highest at night in summer and lowest during daytime in autumn. In particular, the onset of the autumn hunting season induced an abrupt decrease in landscape connectivity.

Conclusions

Human disturbance had a strong impact on roe deer movements, generating pronounced spatio-temporal variation in landscape connectivity. However, high connectivity at night across all seasons implies that Europe’s most abundant and widespread large herbivore potentially plays a key role in transporting ticks, seeds and nutrients among habitats.

Context

Disturbances create spatial variation in environments that may influence animal foraging. Granivory by rodents can influence seed supply and thus plant establishment. However, effects of disturbance patterns on rodent seed removal in western North American conifer forests are generally unknown.

Objectives

We conducted a study in lodgepole pine (Pinus contorta var. latifolia) forests of Greater Yellowstone (Wyoming, USA) to answer: (1) How do seed removal and rodent activity vary between recently burned and adjacent unburned forests and with distance from fire perimeter? (2) Which microhabitat conditions explain variability in seed removal and rodent activity?

Methods

One or two years after wildfires, we established transects (n = 23) with four stations each: at 10 and 40 m from the fire perimeter in both burned and unburned forest. At stations, we deployed trays with lodgepole pine seeds and cameras pointed at trays for 28 days and quantified habitat structure and seed abundance.

Results

Seed removal, which averaged 85%, and diurnal rodent activity did not differ between burned and unburned forests or with distance from the fire perimeter; however, nocturnal rodent activity was lower in burned forests. Seed removal and diurnal rodent activity were not associated with any microhabitat conditions we measured. However, nocturnal rodent activity was associated with microhabitat in both burned and unburned forests.

Conclusions

High seed removal rates suggested that rodent foraging was not reduced by high-severity wildfire. If observed seed removal represents natural conditions, post-dispersal seed predation could influence post-fire recruitment of a widespread foundation tree species.

Background

Recent years have seen an increase in methods for plant phenotyping using image analyses. These methods require new software solutions for data extraction and treatment. These solutions are instrumental in supporting various research pipelines, ranging from the localisation of cellular compounds to the quantification of tree canopies. However, due to the variety of existing tools and the lack of central repository, it is challenging for researchers to identify the software that is best suited for their research.

Results

We present an online, manually curated, database referencing more than 90 plant image analysis software solutions. The website, plant-image-analysis.org, presents each software in a uniform and concise manner enabling users to identify the available solutions for their experimental needs. The website also enables user feedback, evaluations and new software submissions.

Conclusions

The plant-image-analysis.org database provides an overview of existing plant image analysis software. The aim of such a toolbox is to help users to find solutions, and to provide developers a way to exchange and communicate about their work.

Context

The ecological literature is filled with studies highlighting the importance of both habitat loss and fragmentation on biodiversity. The patch concept has been central to these findings, being also at the heart of many ecological theories. Recently, the habitat amount hypothesis has been proposed as an alternative, where the patch concept is put to a rest, and both patch size and patch isolation effects on species richness are reduced to a single gradient: habitat loss in the landscape.

Objectives

As this theory stated clear predictions that could be experimentally tested, many formal tests of the hypothesis have been published recently and this study aims at synthesizing their results.

Methods

A meta-analysis of 13 tests of the habitat amount hypothesis was conducted, to produce a single combined test of the theory.

Results

The 13 tests combined suggest that effects of patch size and isolation, while controlling for habitat amounts, do exist although their overall effect is weak (r?=?0.158).

Conclusions

Literal interpretations of the habitat amount hypothesis, where patch size and isolation have absolutely no effect on species richness, are probably oversimplifications of the processes at work. Still, the theory could prove useful as a baseline of the effects of habitat loss, against which patch size and isolation effects must be contrasted.

Context

Landscape and habitat filters are major drivers of biodiversity of small habitat islands by influencing dispersal and extinction events in plant metapopulations.

Objectives

We assessed the effects of landscape and habitat filters on the species richness, abundance and trait composition of grassland specialist and generalist plants in small habitat islands. We studied traits related to functional spatial connectivity (dispersal ability by wind and animals) and temporal connectivity (clonality and seed bank persistence) using model selection.

Methods

We sampled herbaceous plants, landscape (local and regional isolation) and habitat filters (inclination, woody encroachment and disturbance) in 82 grassland islands in Hungary.

Results

Isolation decreased the abundance of good disperser specialist plants due to the lack of directional vectors transferring seeds between suitable habitat patches. Clonality was an effective strategy, but persistent seed bank did not support the survival of specialist plants in isolated habitats. Generalist plants were unaffected by landscape filters due to their wide habitat breadth and high propagule availability. Clonal specialist plants could cope with increasing woody encroachment due to their high resistance against environmental changes; however, they could not cope with intensive disturbance. Steep slopes providing environmental heterogeneity had an overall positive effect on species richness.

Conclusions

Specialist plants were influenced by the interplay of landscape filters influencing their abundance and habitat filters affecting species richness. Landscape filtering by isolation influenced the abundance of specialist plants by regulating seed dispersal. Habitat filters sorted species that could establish and persist at a site by influencing microsite availability and quality.

Context

Primates are an important component of biodiversity in tropical regions. However, many studies on the effects of habitat change on primates ignore the relative influence of landscape composition and configuration.

Objectives

This study addresses the question: how important are landscape-scale forest area and composition relative to patch-scale (1–1080 ha) and site-scale (transect of 1 km) habitat variables for the occupancy and abundance of four primate species in the Colombian Llanos.

Methods

Using a randomly stratified survey design, 81 fragments were surveyed for primate occupancy and abundance. We used zero-inflated models to test the relative influence of landscape-scale, patch-scale and site-scale variables on occupancy and abundance for each species. A 95% confidence set of models was constructed using the cumulative Akaike weight for each model and the relative importance of each set of variables calculated for each primate species.

Results

Occupancy was determined by a combination of site-scale, patch-scale and landscape-scale variables but this varied substantially among the primate species.

Conclusion

Our study highlights the importance of managing primates at a range of scales that considers the relative importance of site-, patch- and landscape-scale variables.

Context

In response to predominantly local and private approaches to landscape change, landscape ecologists should critically assess the multiscalar influences on landscape design.

Objectives

This study develops a governance framework for Nassauer and Opdam’s “Design-in-Science” model. Its objective is to create an approach for examining hierarchical constraints on landscape design in order to investigate linkages among urban greening initiatives, patterns of landscape change, and the broader societal values driving those changes. It aims to provide an integrative and actionable approach for landscape sustainability science.

Methods

This framework is examined through an ethnographic study of public policy processes surrounding the urban tree initiatives in Boston, MA; Philadelphia, PA; and Baltimore, MD.

Results

These initiatives demonstrate the impact of political and economic decentralization on urban landscape patterns. Their collaborative governance approach incorporates diverse resources to implement programming at a fine-scale. The predominant tree giveaway program fragments the urban and regional forest.

Conclusion

Spatial and temporal fragmentation undermines the long-term security of urban greening programs, and it suggests reconsideration of the role of state regimes in driving broad scale spatial planning.

Context

Seed-dispersing animals often move along “linear gaps” (linear anthropogenic features such as roads and trails that contain little vegetation), especially in densely-vegetated landscapes. As a result, linear gaps and their verges may receive more seeds than adjacent habitats. In addition, linear gap verges may provide more suitable conditions for plant establishment than neighboring habitats. In this way, linear gaps may increase plant abundance and diversity, and facilitate connectivity of native and non-native plant populations, ultimately increasing plant diversity in the landscape.

Objectives

We reviewed current evidence for the potential of anthropogenic linear gaps to increase plant abundance and diversity, and for the mechanisms involved.

Methods

We reviewed peer-reviewed literature published up to December 31st, 2014.

Results

Most (69.2 %) studies found significantly higher plant abundance and/or diversity in linear gap verges than in adjacent habitats. This suggests that linear gaps can increase plant abundance and diversity, and possibly facilitate population spread. However, there was a strong bias toward the study of exotic species. In addition, there were few mechanistic studies to allow estimation of the relative contributions of dispersal and post-dispersal mechanisms operating in linear gaps.

Conclusions

Future studies should focus on entire plant communities, not just exotic species, and should allow identification of the mechanisms by which linear gaps increase plant abundance and diversity. With this knowledge in hand, we will be in a better position to understand whether the net benefit of linear gaps for plant diversity in general outweigh their facilitation of the spread of exotic species.

Background

Accurately segmenting vegetation from the background within digital images is both a fundamental and a challenging task in phenotyping. The performance of traditional methods is satisfactory in homogeneous environments, however, performance decreases when applied to images acquired in dynamic field environments.

Results

In this paper, a multi-feature learning method is proposed to quantify vegetation growth in outdoor field conditions. The introduced technique is compared with the state-of the-art and other learning methods on digital images. All methods are compared and evaluated with different environmental conditions and the following criteria: (1) comparison with ground-truth images, (2) variation along a day with changes in ambient illumination, (3) comparison with manual measurements and (4) an estimation of performance along the full life cycle of a wheat canopy.

Conclusion

The method described is capable of coping with the environmental challenges faced in field conditions, with high levels of adaptiveness and without the need for adjusting a threshold for each digital image. The proposed method is also an ideal candidate to process a time series of phenotypic information throughout the crop growth acquired in the field. Moreover, the introduced method has an advantage that it is not limited to growth measurements only but can be applied on other applications such as identifying weeds, diseases, stress, etc.

Context

Understanding habitat selection can be challenging for species surviving in small populations, but is needed for landscape-scale conservation planning.

Objectives

We assessed how European bison (Bison bonasus) habitat selection, and particularly forest use, varies across subpopulations and spatial scales.

Methods

We gathered the most comprehensive European bison occurrence dataset to date, from five free-ranging herds in Poland. We compared these data to a high-resolution forest map and modelled the influence of environmental and human-pressure variables on habitat selection.

Results

Around 65% of European bison occurrences were in forests, with cows showing a slightly higher forest association than bulls. Forest association did not change markedly across spatial scales, yet differed strongly among herds. Modelling European bison habitat suitability confirmed forest preference, but also showed strong differences in habitat selection among herds. Some herds used open areas heavily and actively selected for them. Similarly, human-pressure variables were important in all herds, but some herds avoided human-dominated areas more than others.

Conclusions

Assessing European bison habitat across multiple herds revealed a more generalist habitat use pattern than when studying individual herds only. Our results highlight that conflicts with land use and people could be substantial if bison are released in human-dominated landscapes. Future restoration efforts should target areas with low road and human population density, regardless of the degree of forest cover. More broadly, our study highlights the importance of considering multiple subpopulations and spatial scales in conservation planning.

Context

Revealing the interaction between landscape pattern and urban land surface temperature (LST) can provide insight into mitigating thermal environmental risks. However, there is no consensus about the key landscape indicators influencing LST.

Objectives

This study sought to identify the key landscape indicators influencing LST considering a large number of landscape pattern variables and multiple scales.

Methods

This study applied ordinary least squares regression and partial least squares regression to explore a combination of landscape metrics and identify the key indicators influencing LST. A total of 49 Landsat images of the main city of Shenzhen, China were examined at 13 spatial scales.

Results

The landscape composition indicators derived from biophysical proportion, a new metric developed in this study, more effectively determined LST variation than those derived from land cover proportion. Area-related landscape configuration indicators independently characterized LST variation, but did not give much more new information beyond that given by land cover proportion. Shape-related landscape configuration indicators were effective in combination with land cover proportion, but their importance was uncertain when temporal and spatial scales varied.

Conclusions

The influence of landscape configuration on LST exists but should not be overestimated. Comparison of numerous variables at multiple spatiotemporal scales can help identify the influence of multiple landscape characteristics on LST variation.

Background

Despite increasing demand, imaging the internal structure of plant organs or tissues without the use of transgenic lines expressing fluorescent proteins remains a challenge. Techniques such as magnetic resonance imaging, optical projection tomography or X-ray absorption tomography have been used with various success, depending on the size and physical properties of the biological material.

Results

X-ray in-line phase tomography was applied for the imaging of internal structures of maize seeds at early stages of development, when the cells are metabolically fully active and water is the main cell content. This 3D imaging technique with histology-like spatial resolution is demonstrated to reveal the anatomy of seed compartments with unequalled contrast by comparison with X-ray absorption tomography. An associated image processing pipeline allowed to quantitatively segment in 3D the four compartments of the seed (embryo, endosperm, nucellus and pericarp) from 7 to 21 days after pollination.

Conclusion

This work constitutes an innovative quantitative use of X-ray in-line phase tomography as a non-destructive fast method to perform virtual histology and extends the developmental stages accessible by this technique which had previously been applied in seed biology to more mature samples.

Context

Many nearshore species are distributed in habitat patches connected only through larval dispersal. Genetic research has shown some spatial structure of such metapopulations and modeling studies have shed light onto possible patterns of connectivity and barriers. However, little is known about human impact on their spatial structure and patterns of connectivity.

Objectives

We examine the effects of fishing on the spatial and temporal dynamics of metapopulations of sedentary marine species (red sea urchin and red abalone) interconnected by larval dispersal.

Methods

We constructed a metapopulation model to simulate abalone and sea urchin metapopulations experiencing increasing levels of fishing mortality. We performed the modularity analysis on the yearly larval connectivity matrices produced by these simulations, and analyzed the changes of modularity and the formation of modules over time as indicators of spatial structure.

Results

The analysis revealed a strong modular spatial structure for abalone and a weak spatial signature for sea urchin. In abalone, under exploitation, modularity takes step-wise drops on the path to extinction, and modules breakdown into smaller fragments followed by module and later metapopulation collapse. In contrast, sea urchin showed high modularity variation, indicating high- and low-mixing years, but an abrupt collapse of the metapopulation under strong exploitation.

Conclusions

The results identify a disruption in larval connectivity and a pattern of collapse in highly modular nearshore metapopulations. These results highlight the ability of modularity to detect spatial structure in marine metapopulations, which varies among species, and to show early changes in the spatial structure of exploited metapopulations.

Context

Natural regenerating forests are rapidly expanding in the tropics. Forest transitions have the potential to restore biodiversity. Spatial targeting of land use policies could improve the biodiversity benefits of reforesting landscapes.

Objective

We explored the relative importance of landscape attributes in influencing the potential of tree cover increase to restore native woody plant biodiversity at the landscape scale.

Methods

We developed land use scenarios that differed in spatial patterns of reforestation, using the Pangor watershed in the Ecuadorian Andes as a case study. We distinguished between reforestation through natural regeneration of woody vegetation in abandoned fallows and planted forests through managed plantations of exotic species on previously cultivated land. We simulated the restoration of woody plant biodiversity for each scenario using LANDIS-II, a process-based model of forest dynamics. A pair-case comparison of simulated woody plant biodiversity for each scenario was conducted against a random scenario.

Results

Species richness in natural regenerating fallows was considerably higher when occurring in: (i) close proximity to remnant forests; (ii) areas with a high percentage of surrounding forest cover; and (iii) compositional heterogeneous landscapes. Reforestation at intermediate altitudes also positively affected restoration of woody plant species. Planted exotic pine forests negatively affected species restoration.

Conclusions

Our research contributes to a better understanding of the recolonization processes of regenerating forests. We provide guidelines for reforestation policies that aim to conserve and restore woody plant biodiversity by accounting for landscape attributes.

Context

Hedgerows are typical landscape features of high environmental and cultural value that often have been sacrificed for agricultural intensification and scale enlargement.

Objectives

We studied the dynamics of hedgerow quality over time in a case study area renowned for its hedgerow landscapes: South West Devon (UK) answering the following research questions: (1) how does the imperative of scale enlargement affect hedgerow quality? and (2) to what extent can cultural landscape degradation be countered by targeted policies?

Methods

We applied an agent-based modeling approach, parameterized with a site specific survey, to explore and discuss outcomes of future landscape change with stakeholders and co-designed preferred scenarios of landscape change during a workshop.

Results

Outcomes suggested that in the case-study area, scale enlargement has a negative effect on hedgerow quality when agri-environment scheme subsidies (AES) are low. In contrast, if the level of AES enrollment is high, scale enlargement can have a positive effect on hedgerow quality, as large holders are more likely to enroll for AES. Stakeholders acknowledged the need for agricultural intensification, but at the same time valued biodiversity and environmental value of the landscape in South West Devon.

Conclusion

Current AES are able to retain a decent hedgerow quality. With lower AES, scale enlargement can have an invigorative effect on hedgerow quality as land managers of larger farms will be less likely to join AES As an addition to AES, harvesting wood fuel from coppiced hedgerows appears a promising way to incentivize rejuvenating hedgerow management without governmental subsidies.

Context

Wild bee populations are currently under threat, which has led to recent efforts to increase pollinator habitat in North America. Simultaneously, U.S. federal energy policies are beginning to encourage perennial bioenergy cropping (PBC) systems, which have the potential to support native bees.

Objectives

Our objective was to explore the potentially interactive effects of crop composition, total PBC area, and PBC patches in different landscape configurations.

Methods

Using a spatially-explicit modeling approach, the Lonsdorf model, we simulated the impacts of three perennial bioenergy crops (PBC: willow, switchgrass, and prairie), three scenarios with different total PBC area (11.7, 23.5 and 28.8% of agricultural land converted to PBC) and two types of landscape configurations (PBC in clustered landscape patterns that represent realistic future configurations or in dispersed neutral landscape models) on a nest abundance index in an Illinois landscape.

Results

Our modeling results suggest that crop composition and PBC area are particularly important for bee nest abundance, whereas landscape configuration is associated with bee nest abundance at the local scale but less so at the regional scale.

Conclusions

Strategies to enhance wild bee habitat should therefore emphasize the crop composition and amount of PBC.