Volatilomics: a non-invasive technique for screening plant phenotypic traits

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.

     

Diversity–disturbance relationship in forest landscapes

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.

     

An early synthesis of the habitat amount hypothesis

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.

     

Temporal shifts in landscape connectivity for an ecosystem engineer,the roe deer,across a multiple-use landscape

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.

     

Landscape and habitat filters jointly drive richness and abundance of specialist plants in terrestrial habitat islands

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.

     

Microhabitat conditions and landscape pattern explain nocturnal rodent activity,but not seed removal,in burned and unburned lodgepole pine forests

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.

     

The influence of landscape relative to site and patch variables on primate distributions in the Colombian Llanos

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.

     

An online database for plant image analysis software tools

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.

     

Can anthropogenic linear gaps increase plant abundance and diversity?

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.

     

Multi-feature machine learning model for automatic segmentation of green fractional vegetation cover for high-throughput field phenotyping

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.

     

One size does not fit all: European bison habitat selection across herds and spatial scales

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.

     

Activating landscape ecology: a governance framework for design-in-science

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.

     

How does a transforming landscape influence bird breeding success?

Context

The conversion of agricultural landscapes to tree plantations is a major form of landscape transformation worldwide, but its effects on biodiversity, particularly key population processes like reproductive success, are poorly understood.

Objectives

We compared bird breeding success between woodland remnants surrounded by maturing stands of plantation Radiata Pine and a matched set of woodland remnants in semi-cleared grazing land.

Methods

Our study was conducted in the Nanangroe region in south-eastern New South Wales, Australia. Using repeated field measurements, we quantified bird breeding success in 23 woodland remnants; 13 surrounded by Radiata Pine plantations and 10 on farms where remnants were surrounded by semi-cleared grazing land. We matched the attributes of native remnant patches between two types of matrix.

Results

We found that: (1) rates of nesting success of smaller-bodied birds in woodland remnants surrounded by grazing land were significantly higher than in woodland remnants surrounded by pine plantations; and (2) taxa with domed nests were more successful at nesting than species that constructed open cup/bowl nests in woodland remnants within farmlands.

Conclusions

Our findings suggest that bird breeding success in remnant woodland patches is significantly diminished as a result of the conversion of semi-cleared grazing land to pine plantations.

     

Step-wise drops in modularity and the fragmentation of exploited marine metapopulations

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.

     

Assessing wild bees in perennial bioenergy landscapes: effects of bioenergy crop composition,landscape configuration,and bioenergy crop area

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.

     

The sounds of silence: regime shifts impoverish marine soundscapes

Context

Regime shifts are well known for driving penetrating ecological change, yet we do not recognise the consequences of these shifts much beyond species diversity and productivity. Sound represents a multidimensional space that carries decision-making information needed for some dispersing species to locate resources and evaluate their quantity and quality.

Objectives

Here we assessed the effect of regime shifts on marine soundscapes, which we propose has the potential function of strengthening the positive or negative feedbacks that mediate ecosystem shifts.

Methods

We tested whether biologically relevant cues are altered by regime shifts in kelp forests and seagrass systems and how specific such shifted soundscapes are to the type of driver; i.e. local pollution (eutrophication) vs. global change (ocean acidification).

Results

Here, we not only provide the first evidence for regime-shifted soundscapes, but also reveal that the modified cues of shifted ecosystems are similar regardless of spatial scale and type of environmental driver. Importantly, biological sounds can act as functional cues for orientation by dispersing larvae, and observed shifts in soundscape loudness may alter this function.

Conclusions

These results open the question as to whether shifted soundscapes provide a functional role in mediating the positive or negative feedbacks that govern the arrival of species associated with driving change or stasis in ecosystem state.

     

Integrating land cover structure and functioning to predict biodiversity patterns: a hierarchical modelling framework designed for ecosystem management

Context

Land-use/land-cover (LU/LC) dynamics is one of the main drivers of global environmental change. In the last years, aerial and satellite imagery have been increasingly used to monitor the spatial extent of changes in LU/LC, deriving relevant biophysical parameters (i.e. primary productivity, climate and habitat structure) that have clear implications in determining spatial and temporal patterns of biodiversity, landscape composition and ecosystem services.

Objectives

An innovative hierarchical modelling framework was developed in order to address the influence of nested attributes of LU/LC on community-based ecological indicators.

Methods

Founded in the principles of the spatially explicit stochastic dynamic methodology (StDM), the proposed methodological advances are supported by the added value of integrating bottom-up interactions between multi-scaled drivers.

Results

The dynamics of biophysical multi-attributes of fine-scale subsystem properties are incorporated to inform dynamic patterns at upper hierarchical levels. Since the most relevant trends associated with LU/LC changes are explicitly modelled within the StDM framework, the ecological indicators’ response can be predicted under different social-economic scenarios and site-specific management actions. A demonstrative application is described to illustrate the framework methodological steps, supporting the theoretic principles previously presented.

Conclusions

We outline the proposed multi-model framework as a promising tool to integrate relevant biophysical information to support ecosystem management and decision-making.

     

Teaching landscape ecology: the importance of field-oriented,inquiry-based approaches

Context

Landscape ecology has traditionally been taught through theoretical classes or computer labs. On the other hand, field labs have been generally less used as a way of teaching landscape ecology concepts.

Objectives

We show that field labs with an inquiry-based approach, where students are involved in the investigation, are feasible for training students in landscape ecology. We evaluated how common field labs are in landscape ecology courses, and also their contribution for student learning.

Methods

We evaluated whether field labs are used in landscape ecology courses by scanning available syllabi. We also used outcomes from a course offered in Brazil to show how field labs can be integrated into landscape ecology courses.

Results

Only 18.2 % of the 44 syllabi we found had field labs. The case study developed in Brazil showed that field labs allowed students to develop important skills, including the ability to design field studies, choose appropriate scales of analysis, detect ecological patterns, and judge multiple hypotheses.

Conclusions

Field labs are still uncommon in landscape ecology courses, but they can be a useful tool to teach landscape ecology concepts and to help students developing the necessary skills to do research. We offer recommendations regarding how to incorporate field labs in landscape ecology courses.