Plant–microbe interactions at multiple scales across a high-elevation landscape

Here we review the numerous studies of plant–microbe interactions conducted at the Niwot Ridge LTER site in Colorado, USA. By synthesising work at scales ranging from the rhizosphere to the landscape, we offer a mechanistic view of how these interactions are essential to understanding the spatial and temporal structuring of plant and microbial communities across this diverse and changing landscape. These new insights are also important for making predictions about how both plant and microbial communities and populations will respond to future changes in this environment, especially with regard to the potential uphill movement of plants and microbes in response to climate change and nitrogen deposition. We predict that the uphill movement of plants and microbes will be especially apparent, and have the most impact, in areas of the alpine that are now mostly plant free. These areas are currently undergoing a shift from a microbe-dominated ecosystem to one where microbe–plant interactions will play a critical role in reducing nutrient losses to downstream ecosystems.     

Testing heterogeneity–diversity relationships in tropical forest restoration

Restoring small-scale habitat heterogeneity in highly diverse systems, like tropical forests, is a conservation challenge and offers an excellent opportunity to test factors affecting community assembly. We investigated whether (1) the applied nucleation restoration strategy (planting tree islands) resulted in higher habitat heterogeneity than more homogeneous forest restoration approaches, (2) increased heterogeneity resulted in more diverse tree recruitment, and (3) the mean or coefficient of variation of habitat variables best explained tree recruitment. We measured soil nutrients, overstory and understory vegetation structure, and tree recruitment at six sites with three 5- to 7-year-old restoration treatments: control (no planting), planted tree islands, and conventional, mixed-species tree plantations. Canopy openness and soil base saturation were more variable in island treatments than in controls and plantations, whereas most soil nutrients had similar coefficients of variation across treatments, and bare ground was more variable in control plots. Seedling and sapling species density were equivalent in plantations and islands, and were substantially higher than in controls. Species spatial turnover, diversity, and richness were similar in island and plantation treatments. Mean canopy openness, rather than heterogeneity, explained the largest proportion of variance in species density. Our results show that, whereas canopy openness and soil base saturation are more heterogeneous with the applied nucleation restoration strategy, this pattern does not translate into greater tree diversity. The lack of a heterogeneity–diversity relationship is likely due to the fact that recruits respond more strongly to mean resource gradients than variability at this early stage in succession, and that seed dispersal limitation likely reduces the available species pool. Results show that planting tree islands facilitates tree recruitment to a similar degree as intensive plantation-style restoration strategies.     

Carbon–biodiversity relationships in a highly diverse subtropical forest

Carbon-focused climate mitigation strategies are becoming increasingly important in forests. However, with ongoing biodiversity declines we require better knowledge of how much such strategies account for biodiversity. We particularly lack information across multiple trophic levels and on established forests, where the interplay between carbon stocks, stand age, and tree diversity might influence carbon–biodiversity relationships. Using a large dataset (>4600 heterotrophic species of 23 taxonomic groups) from secondary, subtropical forests, we tested how multitrophic diversity and diversity within trophic groups relate to aboveground, belowground, and total carbon stocks at different levels of tree species richness and stand age. Our study revealed that aboveground carbon, the key component of climate-based management, was largely unrelated to multitrophic diversity. By contrast, total carbon stocks—that is, including belowground carbon—emerged as a significant predictor of multitrophic diversity. Relationships were nonlinear and strongest for lower trophic levels, but nonsignificant for higher trophic level diversity. Tree species richness and stand age moderated these relationships, suggesting long-term regeneration of forests may be particularly effective in reconciling carbon and biodiversity targets. Our findings highlight that biodiversity benefits of climate-oriented management need to be evaluated carefully, and only maximizing aboveground carbon may fail to account for biodiversity conservation requirements.     

Two lowland stream riffles – linkages between physical habitats and macroinvertebrates across multiple spatial scales

The physical structure of two riffles in a lowland Danish stream was studied and its importance for the composition and density of the macroinvertebrate communities was evaluated. The two riffles were visually assessed to be very similar, but measurements revealed that they differed in overall hydraulic conditions, stability, substratum composition and consolidation. Differences affected abundance of both burrowing and surface dwelling macroinvertebrates. The unstable unconsolidated riffle had higher total macroinvertebrate abundance (4137 m⁻² vs. 1698 m⁻²), diptera abundance (2329 m⁻² vs. 386 m⁻²) and total estimated species richness (31.7 vs. 28.8) as well as lower evenness (0.77 vs. 0.83) than the compact riffle. Among samples within the unconsolidated riffle, variations in macroinvertebrate communities were related to differences in mean substratum particle size. Here a linear log–log relationship existed between macroinvertebrate abundance, the abundance of EPT taxa and the median particle size (r ² _total = 0.46, p = 0.002; r ² _EPT = 0.73, p < 0.001). No similar relationships were evident on the consolidated riffle. Moreover, macroinvertebrate communities on the unconsolidated riffle were dominated by species with a high colonising potential. Despite being assessed to the same morphological unit, physical variation between riffles was surprisingly high as the riffles differed substantially with respect to consolidation, substratum heterogeneity and overall hydraulic structure. Macroinvertebrate community structure and composition also differed between riffles despite being drawn from the same species pool. The findings address the question if we use the correct methods and parameters when assessing the macroinvertebrate communities at the scale of the morphological unit.     

Local–regional species richness relationships are linear at very small to large scales in west-central Pacific corals

If local communities are saturated with species, the relationship between local and regional species richness [the local species richness (LSR)–regional species richness (RSR) relationship] is predicted to become increasingly curvilinear at more local spatial scales. This study tested whether the LSR–RSR relationship for coral species was linear or curvilinear at three local scales across the west-central Pacific Ocean, along a regional biodiversity gradient that includes the world’s most diverse coral assemblages. The local scales comprised transects 10^0–2 m apart, sites 10^3–4 m apart and islands 10^4–6 m apart. The LSR–RSR relationship was never significantly different from linear at any scale. When the Chao1 estimator was used to predict true RSR and LSR, all relationships were also strongly linear. We conclude that local assemblages are open to regional influences even when the local scale is very small relative to the regional scale, and even in extraordinarily rich regions.     

Enhancing the structural diversity between forest patches—A concept and real-world experiment to study biodiversity,multifunctionality and forest resilience across spatial scales

Intensification of land use by humans has led to a homogenization of landscapes and decreasing resilience of ecosystems globally due to a loss of biodiversity, including the majority of forests. Biodiversity–ecosystem functioning (BEF) research has provided compelling evidence for a positive effect of biodiversity on ecosystem functions and services at the local (α-diversity) scale, but we largely lack empirical evidence on how the loss of between-patch β-diversity affects biodiversity and multifunctionality at the landscape scale (γ-diversity). Here, we present a novel concept and experimental framework for elucidating BEF patterns at α-, β-, and γ-scales in real landscapes at a forest management-relevant scale. We examine this framework using 22 temperate broadleaf production forests, dominated by Fagus sylvatica. In 11 of these forests, we manipulated the structure between forest patches by increasing variation in canopy cover and deadwood. We hypothesized that an increase in landscape heterogeneity would enhance the β-diversity of different trophic levels, as well as the β-functionality of various ecosystem functions. We will develop a new statistical framework for BEF studies extending across scales and incorporating biodiversity measures from taxonomic to functional to phylogenetic diversity using Hill numbers. We will further expand the Hill number concept to multifunctionality allowing the decomposition of γ-multifunctionality into α- and β-components. Combining this analytic framework with our experimental data will allow us to test how an increase in between patch heterogeneity affects biodiversity and multifunctionality across spatial scales and trophic levels to help inform and improve forest resilience under climate change. Such an integrative concept for biodiversity and functionality, including spatial scales and multiple aspects of diversity and multifunctionality as well as physical and environmental structure in forests, will go far beyond the current widely applied approach in forestry to increase resilience of future forests through the manipulation of tree species composition.     

Individual flowering phenology shapes plant–pollinator interactions across ecological scales affecting plant reproduction

The balance of pollination competition and facilitation among co-flowering plants and abiotic resource availability can modify plant species and individual reproduction. Floral resource succession and spatial heterogeneity modulate plant–pollinator interactions across ecological scales (individual plant, local assemblage, and interaction network of agroecological infrastructure across the farm). Intraspecific variation in flowering phenology can modulate the precise level of spatio-temporal heterogeneity in floral resources, pollen donor density, and pollinator interactions that a plant individual is exposed to, thereby affecting reproduction. We tested how abiotic resources and multi-scale plant–pollinator interactions affected individual plant seed set modulated by intraspecific variation in flowering phenology and spatio-temporal floral heterogeneity arising from agroecological infrastructure. We transplanted two focal insect-pollinated plant species (Cyanus segetum and Centaurea jacea, n = 288) into agroecological infrastructure (10 sown wildflower and six legume–grass strips) across a farm-scale experiment (125 ha). We applied an individual-based phenologically explicit approach to match precisely the flowering period of plant individuals to the concomitant level of spatio-temporal heterogeneity in plant–pollinator interactions, potential pollen donors, floral resources, and abiotic conditions (temperature, water, and nitrogen). Individual plant attractiveness, assemblage floral density, and conspecific pollen donor density (C. jacea) improved seed set. Network linkage density increased focal species seed set and modified the effect of local assemblage richness and abundance on C. segetum. Mutual dependence on pollinators in networks increased C. segetum seed set, while C. jacea seed set was greatest where both specialization on pollinators and mutual dependence was high. Abiotic conditions were of little or no importance to seed set. Intra- and interspecific plant–pollinator interactions respond to spatio-temporal heterogeneity arising from agroecological management affecting wild plant species reproduction. The interplay of pollinator interactions within and between ecological scales affecting seed set implies a co-occurrence of pollinator-mediated facilitative and competitive interactions among plant species and individuals.     

Vegetation composition,structure and soil properties across coastal forest–barren ecotones

Coastal barrens support rare plant species but may be threatened by forest encroachment. We determined whether trees spread into coastal barren habitat from forest patches and assessed plant species composition and soil properties across the forest–barren ecotone. We quantified tree age and height, soil properties, and vascular plant, bryophyte and lichen species composition along transects perpendicular to the edges of tree patches within the forest–barren ecotone in coastal Nova Scotia. Randomization tests assessed whether the vegetation and environmental characteristics were significantly different in the transition zone compared to one or both adjoining ecosystems. We used ordination to examine trends in species composition across the ecotone and the relationship to environmental variables. Tree age and height decreased continuously from the forest towards the edge of the forest patches. There were also trends in vegetation composition and structure from the forest into the open barrens. Many species were most abundant within the transition zone, although not always significantly. Soil properties were relatively uniform across the ecotone. The structure and vegetation of the forest–barren ecotone suggests that forest patches act as nuclei for forest expansion on barrens with a typical successional pathway where coastal barren vegetation is gradually replaced by forest species. This encroachment may pose a threat to rare barrens communities. While landscape factors such as salt spray and wind exposure may determine the general locations where forest can establish, biotic processes of growth and dispersal appear to govern the fine-scale expansion of tree patches.     

Edge effect and species–area relationships in the gall-forming insect fauna of natural forest patches in the Brazilian Pantanal

The aim of this study was to (i) measure differences in species richness between edge habitats versus interior habitats, or more precisely the edge effect, and (ii) test the species–area relationship for gall-forming insects in natural forest patches in a Brazilian floodplain (Pantanal of Mato Grosso do Sul). These patches are regionally known as capões, basically composed of woody vegetation. Twenty-seven patches were surveyed. In each patch two transects were conducted for gall sampling. One transect encircled the patches while the other was conducted in the interior of the patch, totaling 54h of sampling. Host plant and galling insect species composition differed quite characteristically between the edge and the interior of patches, but galling insect richness did not. When insect gall richness was expressed as the ratio between insect gall and host plant richness (gall per plant ratio), a weak species–area relationship was found. Our results suggest that the number of galling insects per individual plant is not affected by the size of the patch. Despite these results, the natural forest patches found in this region seem well suited for long-term studies addressing species–area relationships. With regard to herbivorous insects, these studies should be combined with research on host plant dynamics during flooding and dry seasons.     

Sensory-based niche partitioning in a multiple predator–multiple prey community

Many predators and parasites eavesdrop on the communication signals of their prey. Eavesdropping is typically studied as dyadic predator–prey species interactions; yet in nature, most predators target multiple prey species and most prey must evade multiple predator species. The impact of predator communities on prey signal evolution is not well understood. Predators could converge in their preferences for conspicuous signal properties, generating competition among predators and natural selection on particular prey signal features. Alternatively, predator species could vary in their preferences for prey signal properties, resulting in sensory-based niche partitioning of prey resources. In the Neotropics, many substrate-gleaning bats use the mate-attraction songs of male katydids to locate them as prey. We studied mechanisms of niche partitioning in four substrate-gleaning bat species and found they are similar in morphology, echolocation signal design and prey-handling ability, but each species preferred different acoustic features of male song in 12 sympatric katydid species. This divergence in predator preference probably contributes to the coexistence of many substrate-gleaning bat species in the Neotropics, and the substantial diversity in the mate-attraction signals of katydids. Our results provide insight into how multiple eavesdropping predator species might influence prey signal evolution through sensory-based niche partitioning.     

Linking stream habitats and spider distribution: spatial variations in trophic transfer across a forest–stream boundary

In headwater streams, many aquatic insects rely on terrestrial detritus, while their emergence from streams often subsidizes riparian generalist predators. However, spatial variations in such reciprocal trophic linkages remain poorly understood. The present study, conducted in a northern Japanese stream and the surrounding forest, showed that pool–riffle structure brought about heterogeneous distributions of detritus deposits and benthic aquatic insects. The resulting variations in aquatic insect emergence influenced the distributions of riparian web-building spiders. Pools with slow current stored greater amounts of detritus than riffles, allowing more benthic aquatic insects to develop in pools. The greater larval biomass in pools and greater tendency for riffle insects to drift into pools at metamorphosis resulted in an emergence rate of aquatic insects from pools that was some four to five times greater than from riffles. In the riparian forest, web-building spiders (Tetragnathidae and Linyphiidae) were distributed in accordance with the emergence rates of aquatic insects, upon which both spider groups heavily depended. Consequently, the riparian strips bordering pools had a density of tetragnathid spiders that was twice as high as that of the riparian strips adjacent to riffles. Moreover, although limitations of vegetation structure prevented the aggregation of linyphiid spiders around pools, linyphiid density normalized by shrub density was higher in habitats adjacent to pools than those adjacent to riffles. The results indicated that stream geomorphology, which affects the storage of terrestrial organic material and the export of such material to riparian forests via aquatic insect emergence, plays a role in determining the strength of terrestrial–aquatic linkages in headwater ecosystems.     

What determines variation in home range size across spatiotemporal scales in a large browsing herbivore?

1. Most studies of intraspecific variation in home range size have investigated only a single or a few factors and often at one specific scale. However, considering multiple spatial and temporal scales when defining a home range is important as mechanisms that affect variation in home range size may differ depending on the scale under investigation. 2. We aim to quantify the relative effect of various individual, forage and climatic determinants of variation in home range size across multiple spatiotemporal scales in a large browsing herbivore, the moose (Alces alces), living at the southern limit of its distribution in Norway. 3. Total home range size and core home range areas were estimated for daily to monthly scales in summer and winter using both local convex hull (LoCoH) and fixed kernel home range methods. Variance in home range size was analysed using linear mixed-effects models for repeated measurements. 4. Reproductive status was the most influential individual-level factor explaining variance in moose home range size, with females accompanied by a calf having smaller summer ranges across all scales. Variation in home range size was strongly correlated with spatiotemporal changes in quantity and quality of natural food resources. Home range size decreased with increasing browse density at daily scales, but the relationship changed to positive at longer temporal scales. In contrast, browse quality was consistently negatively correlated with home range size except at the monthly scale during winter when depletion of high-quality forage occurs. Local climate affected total home range size more than core areas. Temperature, precipitation and snow depth influenced home range size directly at short temporal scales. 5. The relative effects of intrinsic and extrinsic determinants of variation in home range size differed with spatiotemporal scale, providing clear evidence that home range size is scale dependent in this large browser. Insight into the behavioural responses of populations to climatic stochasticity and forage variability is essential in view of current and future climate change, especially for populations with thermoregulatory restrictions living at the southern limit of their distribution.     

Positive diversity–invasibility relationship in species-rich semi-natural grassland at the neighbourhood scale

Background and Aims

Attempts to answer the old question of whether high diversity causes high invasion resistance have resulted in an invasion paradox: while large-scale studies often find a positive relationship between diversity and invasibility, small-scale experimental studies often find a negative relationship. Many of the small-scale studies are conducted in artificial communities of even-aged plants. Species in natural communities, however, do not represent one simultaneous cohort and occur at various levels of spatial aggregation at different scales. This study used natural patterns of diversity to assess the relationship between diversity and invasibility within a uniformly managed, semi-natural community.

Methods

In species-rich grassland, one seed of each of ten species was added to each of 50 contiguous 16 cm² quadrats within seven plots (8 × 100 cm). The emergence of these species was recorded in seven control plots, and establishment success was measured in relation to the species diversity of the resident vegetation at two spatial scales, quadrat (64 cm²) within plots (800 cm²) and between plots within the site (approx. 400 m²) over 46 months.

Key Results

Invader success was positively related to resident species diversity and richness over a range of 28–37 species per plot. This relationship emerged 7 months after seed addition and remained over time despite continuous mortality of invaders.

Conclusions

Biotic resistance to plant invasion may play only a sub-ordinate role in species-rich, semi-natural grassland. As possible alternative explanations for the positive diversity–invasibility relationship are not clear, it is recommended that future studies elaborate fine-scale environmental heterogeneity in resource supplies or potential resource flows from resident species to seedlings by means of soil biological networks established by arbuscular mycorrhizal fungi.     

Structure–function relationships in HIV-1 Nef

The accessory Nef protein of HIV and SIV is essential for viral pathogenesis, yet it is perplexing in its multitude of molecular functions. In this review we analyse the structure–function relationships of motifs recently proposed to play roles in aspects of Nef modification, signalling and trafficking, and thereby to impinge on the ability of the virus to survive in, and to manipulate, its cellular host. Based on the full-length structure assembly of HIV Nef, we correlate surface accessibility with secondary structure elements and sequence conservation. Motifs involved in Nef-mediated CD4 and MHC I downregulation are located in flexible regions of Nef, suggesting that the formation of the transient trafficking complexes involved in these processes depends on the recognition of primary sequences. In contrast, the interaction sites for signalling molecules that contain SH3 domains or the p21-activated kinases are associated with the well folded core domain, suggesting the recognition of highly structured protein surfaces.     

Temporally variable macroinvertebrate–stone relationships in streams

Stones were used to sample macroinvertebrates and characterise microhabitats at monthly or bimonthly intervals in six Ecuadorian streams covering a gradient in four different stability measures and other stream characteristics. The physical variables current velocity, water depth, horizontal position, embeddedness and size were measured to characterise stone microhabitats and presumed to be affected by or related to physical impact during hydrological disturbances. My first objective was to analyse how density, the number of families and a richness measure (residuals from a power regression of families vs. individuals) were related to the physical characteristics of individual stone habitats. My second objective was to quantify temporal variability in fauna–stone relationships and to analyse if such variability was related to overall stability of stream reaches. Partial Least Squares (PLS) multiple regression analyses showed high temporal variability between sampling dates in factor loadings of specific stone micro habitat variables. In spite of this, there was a clear negative effect of depth and a positive effect of current on density and number of families. Stone size was consistently negatively related to density and positively related to number of families. Patterns were less clear for richness residuals. Simple linear regressions of fauna vs. stone parameters generally confirmed the results reached by the PLS analysis, although few of the regressions were significant. For all fauna–stone regressions the variability in slopes was much higher among sampling dates within streams (temporal variability) than among streams (spatial variability), and significant slopes were even inverted on different sampling dates. Although the coefficients of variation (CV) of slopes of a given combination of fauna parameter and stone variable from different sampling dates (n=9–11) were rarely correlated to any of the measures of stream stability, this study has demonstrated high temporal variability in fauna–stone relationships (CV’s of regression slopes). Consequently, temporally un-replicated studies of such relationships do not necessarily reveal general patterns.     

Are fragments islands? Landscape context and density-area relationships in boreal forest birds

We investigated the role of matrix type as a determinant of change in bird densities with forest patch area (patch area effect) in two different Fennoscandian landscape types: mature forest fragments surrounded by cut-over or regenerating forest and true forested islands surrounded by water. Since the matrix of forested archipelagoes offers no resources to and impedes movement of forest birds, we predict that patch area effects on bird densities should be stronger on forested islands than in forest patches fragmented by forestry. We compiled correlation estimates of the bird density-patch area relationship from the literature and analyzed the data using meta-analysis. Combined correlation coefficients were significantly positive on islands but were not significantly different from 0 in fragments. Within-species comparisons also showed that correlations were consistently more positive on islands than in fragments. On islands but not in fragments, the densities of forest specialist species were more sensitive to area than were the densities of forest generalists, suggesting that specialists are more sensitive to changes in matrix quality. Migration status was only weakly associated with bird responses to island or fragment area. Thus, forest fragments do not function as true islands. We interpret this as the result of compensatory effects of the surrounding matrix in terms of availability of resources and enhanced connectivity (matrix quality hypothesis). A purely patch-centered approach seems an unrealistic framework to analyze population processes occurring in complex landscapes. The characteristics of the habitat matrix should therefore be explicitly incorporated into the assessment of species' responses to habitat fragmentation.     

Evaluating δ15N–body size relationships across taxonomic levels using hierarchical models

Ecologists routinely set out to estimate the trophic position of individuals, populations, and species composing food webs, and nitrogen stable isotopes (δ¹⁵N) are a widely used proxy for trophic position. Although δ¹⁵N values are often sampled at the level of individuals, estimates and confidence intervals are frequently sought for aggregations of individuals. If individual δ¹⁵N values are correlated as an artifact of sampling design (e.g., clustering of samples in space or time) or due to intrinsic groupings (e.g., life history stages, social groups, taxonomy), such estimates may be biased and exhibit overly optimistic confidence intervals. However, these issues can be accommodated using hierarchical modeling methods. Here, we demonstrate how hierarchical models offer an additional quantitative tool for investigating δ¹⁵N variability and we explicitly evaluate how δ¹⁵N varies with body size at successively higher levels of taxonomic aggregation in a diverse fish assemblage. The models take advantage of all available data, better account for uncertainty in parameters estimates, may improve inferences on coefficients corresponding to groups with small to moderate sample sizes, and partition variation across model levels, which provides convenient summaries of the ‘importance’ of each level in terms of unexplained heterogeneity in the data. These methods can easily be applied to diet-based studies of trophic position. Although hierarchical models are well-understood and established tools, their benefits have yet to be fully reaped by stable isotope and food web ecologists. We suggest that hierarchical models can provide a robust framework for conceptualizing and statistically modeling trophic position at multiple levels of aggregation.