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.

     

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.

     

Landscape configuration alters spatial arrangement of terrestrial-aquatic subsidies in headwater streams

Context

Freshwater ecosystems depend on surrounding terrestrial landscape for resources. Most important are terrestrial leaf litter subsidies, which differ depending on land use. We lack a good understanding of the variation of these inputs across spatial scales.

Objectives

We sought to determine: (1) the relative importance of local versus catchment-level forestation for benthic leaf litter biomass in streams, (2) how landscape configuration alters these relationships, and (3) how land use affects the quality and diversity of leaf litter subsidies.

Methods

We measured biomass and identity of benthic leaf litter in 121 reaches in 10 independent catchments seasonally over the course of a year. We assessed direct and indirect effects of forestation, reach position, and seasonality on leaf litter biomass using structural equation models, and assessed how leaf litter diversity varied with land use.

Results

In catchments with forested headwaters, the degree of forestation and reach position in the catchment influenced benthic leaf litter biomass indirectly through local reach-scale forestation. In catchments where forest was only located downstream, or with minimal forest, none of these factors influenced reach-level benthic leaf litter. Leaf litter diversity peaked in fall in all land use types, but was generally lowest in forested reaches.

Conclusions

Not only habitat amount, but its location relative to other habitats is important for ecosystem function in the context of cross-ecosystem material flows. Here, lack of upstream forest altered spatial patterns of leaf litter storage. Studies with high spatiotemporal resolution may further reveal effects of landscape configuration on other ecosystems.

     

Interactions of landscape disturbances and climate change dictate ecological pattern and process: spatial modeling of wildfire,insect, and disease dynamics under future climates

Context

Interactions among disturbances, climate, and vegetation influence landscape patterns and ecosystem processes. Climate changes, exotic invasions, beetle outbreaks, altered fire regimes, and human activities may interact to produce landscapes that appear and function beyond historical analogs.

Objectives

We used the mechanistic ecosystem-fire process model FireBGCv2 to model interactions of wildland fire, mountain pine beetle (Dendroctonus ponderosae), and white pine blister rust (Cronartium ribicola) under current and future climates, across three diverse study areas.

Methods

We assessed changes in tree basal area as a measure of landscape response over a 300-year simulation period for the Crown of the Continent in north-central Montana, East Fork of the Bitterroot River in western Montana, and Yellowstone Central Plateau in western Wyoming, USA.

Results

Interacting disturbances reduced overall basal area via increased tree mortality of host species. Wildfire decreased basal area more than beetles or rust, and disturbance interactions modeled under future climate significantly altered landscape basal area as compared with no-disturbance and current climate scenarios. Responses varied among landscapes depending on species composition, sensitivity to fire, and pathogen and beetle suitability and susceptibility.

Conclusions

Understanding disturbance interactions is critical for managing landscapes because forest responses to wildfires, pathogens, and beetle attacks may offset or exacerbate climate influences, with consequences for wildlife, carbon, and biodiversity.

     

Estimating density of a territorial species in a dynamic landscape

Context

Conservation planning for at-risk species requires understanding of where species are likely to occur, how many individuals are likely to be supported on a given landscape, and the ability to monitor those changes through time.

Objectives

We developed a distribution model for northern spotted owls that incorporates both habitat suitability and probability of territory occupancy while accounting for interspecies competition.

Methods

We developed range-wide habitat suitability maps for two time periods (1993 and 2012) for northern spotted owls that accounted for regional differences in habitat use and home range size. We used these maps for a long-term demographic monitoring study area to assess habitat change and estimate the number of potential territories based on available habitat for both time periods. We adjusted the number of potential territories using known occupancy rates to estimate owl densities for both time periods. We evaluated our range-wide habitat suitability model using independent survey data.

Results

Our range-wide habitat maps predicted areas suitable for territorial spotted owl presence well. On the demographic study area, the amount of habitat declined 19.7% between 1993 and 2012, while our estimate of the habitat-based carrying capacity declined from 150 to 146 territories. Estimated number of occupied territories declined from 94 to 57.

Conclusions

Conservation and recovery of at-risk species depends on understanding how habitat changes over time in response to factors such as wildfire, climate change, biological invasions, and interspecies competition, and how these changes influence species distribution. We demonstrate a model-based approach that provides an effective planning tool.

     

Combined effects of area,connectivity, history and structural heterogeneity of woodlands on the species richness of hoverflies (Diptera: Syrphidae)

Context

Hoverflies are often used as bio-indicators for ecosystem conservation, but only few studies have actually investigated the key factors explaining their richness in woodlands.

Objectives

In a fragmented landscape in southwest France, we investigated the joint effects of woodland area, structural heterogeneity, connectivity and history on the species richness of forest-specialist hoverflies, and whether there was a time lag in the response of hoverflies to habitat changes, and tested the effect of spatiotemporal changes.

Methods

Current species richness was sampled in 48 woodlands using 99 Malaise traps. Structural variables were derived from a rapid habitat assessment protocol. Old maps and aerial photographs were used to extract past and present spatial patterns of the woodlands since 1850. Relationships between species richness and explanatory variables were explored using generalized linear models.

Results

We show that current habitat area, connectivity, historical continuity and the average density of tree-microhabitats explained 35 % of variation in species richness. Species richness was affected differently by changes in patch area between 1979 and 2010, depending on woodland connectivity. In isolated woodlands, extinction debt and colonization credit were revealed, showing that even several decades are not sufficient for hoverflies to adapt to landscape-scale habitat conditions.

Conclusions

These findings emphasise the importance of maintaining connectedness between woodlands, which facilitates the dispersion in a changing landscape. Our results also highlight the benefits of using a change-oriented approach to explain the current distribution patterns of species, especially when several spatial processes act jointly.

     

Spatial and temporal variability of fragmentation effects in a long term,eucalypt forest fragmentation experiment

Context

Although forest fragmentation is generally thought to impact tree growth and mortality negatively, recent work suggests some forests are resilient. Experimental forests provide an opportunity to examine the timing and extent of forest tree resilience to disturbance from fragmentation.

Objectives

We used the Wog Wog Habitat Fragmentation Experiment in southeastern Australia to test Eucalyptus growth and survivorship responses to forest fragmentation over a 26 year period.

Methods

We measured 2418 tree diameters and used spline-regression techniques to examine non-monotonic fragmentation effect over two time periods.

Results

Over the first 4 years after fragmentation, individual eucalypt tree growth was greater than in continuous forest for large trees and mortality rates were higher only within 10 m of edges. Over the following 22 years only the effects on tree growth remained and on average all fragments rebounded so that their biomass and mortality rates were equivalent to continuous forest. Importantly non-monotonic patterns were observed in growth and mortality with respect to area and distance from edge in both study periods, demonstrating that fragmentation impacts on trees can be strong in localized areas (greatest in 3 ha fragments and 0–30 m edges) and over short time periods.

Conclusions

Dry-sclerophyll eucalypt forests join the set of forest types that display resilient growth dynamics post fragmentation. Moreover, persistent non-monotonic impacts on tree growth with respect to tree size, fragment area, and fragment distance from edge, highlighting landscape fragmentation as a driver of habitat heterogeneity within remnant forest fragments.

     

Multi-level,multi-scale habitat selection by a wide-ranging,federally threatened snake

Context

Although multi-scale approaches are commonly used to assess wildlife-habitat relationships, few studies have examined selection at multiple spatial scales within different hierarchical levels/orders of selection [sensu Johnson’s (1980) orders of selection]. Failure to account for multi-scale relationships within a single level of selection may lead to misleading inferences and predictions.

Objectives

We examined habitat selection of the federally threatened eastern indigo snake (Drymarchon couperi) in peninsular Florida at the level of the home range (Level II selection) and individual telemetry location (Level III selection) to identify influential habitat covariates and predict relative probability of selection.

Methods

Within each level, we identified the characteristic scale for each habitat covariate to create multi-scale resource selection functions. We used home range selection functions to model Level II selection and paired logistic regression to model Level III selection.

Results

At both levels, EIS selected undeveloped upland land covers and habitat edges while avoiding urban land covers. Selection was generally strongest at the finest scales with the exception of Level II urban edge which was avoided at a broad scale indicating avoidance of urbanized land covers rather than urban edge per se.

Conclusions

Our study illustrates how characteristic scales may vary within a single level of selection and demonstrates the utility of multi-level, scale-optimized habitat selection analyses. We emphasize the importance of maintaining large mosaics of natural habitats for eastern indigo snake conservation.

     

Habitat connectivity and complexity underpin fish community structure across a seascape of tropical macroalgae meadows

Context

In heterogeneous landscapes, local patterns of community structure are a product of the habitat size and condition within a patch interacting with adjacent habitat patches of varying composition and quantity. While evidence for local versus landscape factors have been found in terrestrial biomes, support for such multi-scale effects shaping marine ecological communities is equivocal.

Objectives

We investigated whether within-patch habitat condition can override seascape context to explain the community structure of macroalgae-associated reef fishes across a tropical seascape.

Methods

We mapped the distribution and abundance of a diverse family of reef fishes (Labridae) occupying macroalgae meadows within a tropical reef ecosystem, and using best-subsets model selection, investigated the potential for habitat structural connectivity and/or local habitat quality for predicting variations in fish community structure across the seascape.

Results

Local habitat quality (canopy structure, hard habitat complexity) and area of coral-dominated habitat within 500 m of a macroalgal meadow provided the best predictors of fish community structure. However, the specific importance of a given predictor varied with fish life history stage and functional trophic group. Interestingly, macroalgae meadow area was among the least important predictors.

Conclusions

Given the complex interplay between local habitat quality and spatial context effects on fish biodiversity, our study reveals the multi-scale predictors that should be used in spatial conservation and management approaches for tropical fish diversity. Moreover, our findings question the ubiquity of habitat area effects in patchy landscapes, and cautions against a sole reliance on habitat quantity in spatial management.

     

Environmental drivers of community diversity in a neotropical urban landscape: a multi-scale analysis

Context

Many aquatic communities are linked by the aerial dispersal of multiple, interacting species and are thus structured by processes occurring in both the aquatic and terrestrial compartments of the ecosystem.

Objectives

To evaluate the environmental factors shaping the aquatic macroinvertebrate communities associated with tank bromeliads in an urban landscape.

Methods

Thirty-two bromeliads were georeferenced to assess the spatial distribution of the aquatic meta-habitat in one city. The relative influence of the aquatic and terrestrial habitats on the structure of macroinvertebrate communities was analyzed at four spatial scales (radius = 10, 30, 50, and 70 m) using redundancy analyses.

Results

We sorted 18,352 aquatic macroinvertebrates into 29 taxa. Water volume and the amount of organic matter explained a significant part of the taxa variance, regardless of spatial scale. The remaining variance was explained by the meta-habitat size (i.e., the water volume for all of the bromeliads within a given surface area), the distance to the nearest building at small scales, and the surface area of buildings plus ground cover at larger scales. At small scales, the meta-habitat size influenced the two most frequent mosquito species in opposite ways, suggesting spatial competition and coexistence. Greater vegetation cover favored the presence of a top predator.

Conclusions

The size of the meta-habitat and urban landscape characteristics influence the structure of aquatic communities in tank bromeliads, including mosquito larval abundance. Modifications to this landscape will affect both the terrestrial and aquatic compartments of the urban ecosystem, offering prospects for mosquito management during urban planning.

     

Habitat and food supply across multiple spatial scales influence the distribution and abundance of a nocturnal aerial insectivore

Context

Conservation research often focuses on individual threats at a single spatial scale, but population declines can result from multiple stressors occurring at different spatial scales. Analyses incorporating alternative hypotheses across spatial scales allow more robust evaluation of the ecological processes underlying population declines.

Objectives

Populations of many aerially insectivorous birds are declining, yet conservation efforts remain focused on habitat due to an absence of data on changes in prey availability. We evaluate the potential for prey and habitat availability at multiple spatial scales to influence a population of eastern whip-poor-wills (Antrostomus vociferous).

Methods

We assess relationships between landcover (topographical map and satellite imagery) and insect abundance (moths and beetles from blacklight traps), and whip-poor-will distribution and abundance within eastern Canada using Ontario breeding bird atlas data (1980s and 2000s), acoustic recordings (regional), and point counts (local).

Results

Whip-poor-will occurrence in both atlas time periods was positively associated with forest area and fragmentation, but only a delayed effect of urban area explained reductions in detection. Contemporary regional whip-poor-will presence was positively related to moth abundance, and local whip-poor-will abundance was best predicted by area of open-canopy forest, anthropogenic linear disturbance density, and beetle abundance. Our finding that bird presence and abundance were associated with human activity and insect abundance across spatial scales suggests factors beyond habitat structure are likely driving population declines in whip-poor-wills and other aerial insectivores.

Conclusions

This study demonstrates the importance of examining multiple hypotheses, including seasonally and locally variable food availability, across a range of spatial scales to direct conservation efforts.

     

Using topographic geodiversity to connect conservation lands in the Central Yukon,Alaska

Context

Alaskan landscapes are changing due to climate change impacts. Maintaining or restoring landscape connectivity is a widely suggested climate change adaptation strategy because species are shifting their distributions to align with emerging conditions. Natural resource managers in Alaska have an opportunity to proactively design connected landscapes as infrastructure networks and economic development continue to increase in the state.

Objectives

We provide an example of strategic, multijurisdictional planning to maintain landscape connectivity at a large spatial scale.

Methods

We use geodiversity to model climate-resilient landscape linkages between conservation lands within and adjacent to a 59-million-acre planning area.

Results

The resulting landscape linkage design consists of as little as 1% of the planning area, but can connect over 64 million acres of conservation land allowing the Bureau of Land Management to leverage the current land designations to maximize the conservation value of the entire landscape.

Conclusions

Maintaining landscape connectivity is above and beyond the mandates and responsibilities of a single organization or land owner. Bridging institutions and partnerships, such as the Northwest Boreal Landscape Conservation Cooperative, can facilitate the coordination needed for this type of multi-jurisdictional planning effort. The opportunity to manage proactively, rather than waiting for system degradation and then responding reactively, should not be undervalued. The implementation of this work will serve as a model for other relatively intact systems and moreover showcases the potential of twenty-first century models of conservation and sustainability.

     

Diel leaf growth of soybean: a novel method to analyze two-dimensional leaf expansion in high temporal resolution based on a marker tracking approach (Martrack Leaf)

Background

We present a novel method for quantitative analysis of dicot leaf expansion at high temporal resolution. Image sequences of growing leaves were assessed using a marker tracking algorithm. An important feature of the method is the attachment of dark beads that serve as artificial landmarks to the leaf margin. The beads are mechanically constricted to the focal plane of a camera. Leaf expansion is approximated by the increase in area of the polygon defined by the centers of mass of the beads surrounding the leaf. Fluctuating illumination conditions often pose serious problems for tracking natural structures of a leaf; this problem is circumvented here by the use of the beads.

Results

The new method has been used to assess leaf growth in environmental situations with different illumination conditions that are typical in agricultural and biological experiments: Constant illumination via fluorescent light tubes in a climate chamber, a mix of natural and artificial illumination in a greenhouse and natural illumination of the situation on typical summer days in the field. Typical features of diel (24h) soybean leaf growth patterns were revealed in all three conditions, thereby demonstrating the general applicability of the method. Algorithms are provided to the entire community interested in using such approaches.

Conclusions

The implementation Martrack Leaf presented here is a robust method to investigate diel leaf growth rhythms both under natural and artificial illumination conditions. It will be beneficial for the further elucidation of genotype x environment x management interactions affecting leaf growth processes.

     

Edge effects in tropical dry forests of Madagascar: additivity or synergy?

Context

The study of habitat fragmentation is complex because multiple, potentially synergistic, ecological processes may be acting simultaneously. Further, edge effects themselves may be complex in that additivity from multiple edges can give rise to heterogeneous nearest–edge gradients.

Objectives

We used heat diffusion as a proxy for additive edge effects in two study landscapes in order to test whether two key observations recently attributed to synergy between edge and area effects could be more simply explained by additivity; namely, steeper edge gradients in larger fragments and variation in slopes of species–area relationships as a function of distances to fragment edges.

Methods

We sampled forest structure in northwestern Madagascar at various distances from the edge in fragments and continuous forest and used an inverse modelling approach to parameterize the model. In addition, we applied the model to data from a published study of beetle communities in fragmented forests in New Zealand.

Results

With increasing proximity to edges, woody stem densities decreased and, as predicted, smaller fragments had lower stem densities and less steep edge gradients than larger ones. The model successfully predicted shifts in species–area relationships as a function of nearest–edge distances for beetle species, although observed richness for forest specialists in the smallest fragments was lower than predicted.

Conclusions

Two key observations attributed to synergy between edge and area effects were explained by edge additivity. The model is particularly useful in that it can help to disentangle the complex sets of processes acting in fragmented landscapes.

     

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.

     

Species pool,human population,and global versus regional invasion patterns

Context

Biological invasions are among the greatest global and regional threats to biomes in the Anthropocene. Islands, in particular, have been perceived to have higher vulnerability to invasions. Because of the dynamic nature of ongoing invasions, distinguishing regional patterns from global patterns and their underlying determinants remains a challenge.

Objectives

We aim to comparatively examine global versus regional patterns of plant invasions and the possible underlying mechanisms. We also test whether there is a difference in degree of invasion and invasibility between mainland areas and islands.

Methods

We compiled and analyzed data from published sources for 100 mainland areas (i.e., regions, countries, states, and provinces) and 89 islands across the globe.

Results

We find that (1) the pool of exotic species available intrinsically decreases as area of the land considered increases (at global scale, all is native), thus global invasion patterns assessed by exotic fraction (proportion of exotics) are primarily determined by land area; (2) because “exotic” is defined relative to the borders of the target region, “boundary effects” can result in regional differences in invasion patterns without any ecological processes being involved; and (3) human population density is closely linked to exotic fraction within regions that are defined by a single administrative border.

Conclusions

There were clear differences between global and regional patterns of plant invasions. We observed no difference in the exotic fraction-area relationship between mainland areas and islands, supporting what we refer to as the “island-mainland continuum concept” (i.e., no clear separation in the degree of invasion between islands and mainland area with regard to the effects of area). Because of scale-dependency in many observed patterns, future focus should be placed on the links between local, regional, and global invasion patterns.

     

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.

     

Habitat amount and quality,not patch size,determine persistence of a woodland-dependent mammal in an agricultural landscape

Context

The classical theory of island biogeography explains loss of species in fragmented landscapes as an effect of remnant patch size and isolation. Recently this has been challenged by the habitat amount and habitat continuum hypotheses, according to which persistence in modified landscapes is related to total habitat amount rather than habitat configuration or the ability of species to use all habitats to varying degrees. Distinguishing between these theories is essential for effective conservation planning in modified landscapes.

Objective

Identify which factors of habitat type, amount and configuration predict the persistence of a keystone woodland specialist, the eastern bettong Bettongia gaimardi, in a fragmented landscape.

Method

In the Midlands region of Tasmania we carried out camera surveys at 62 sites in summer and winter. We included habitat and landscape features to model whether habitat amount or patch size and isolation influenced the presence of the eastern bettong, and to measure effects of habitat quality.

Results

Habitat amount within a 1 km buffer was a better predictor of occupancy than patch size and isolation. Occupancy was also affected by habitat quality, indicated by density of regenerating stems.

Conclusion

Our results support the habitat amount hypothesis as a better predictor of presence. For a species that is able to cross the matrix between remnant patches and utilise multiple patches, the island biogeography concept does not explain habitat use in fragmented landscapes. Our results emphasize the value of small remnant patches for conservation of the eastern bettong, provided those patches are in good condition.