Advances, challenges and a developing synthesis of ecological community assembly theory

The effect of soil on spatial variation of the herbaceous layer modulated by overstorey in an Eastern European poplar-willow forest

The tree species composition can influence the dynamics of herbaceous species and enhance the spatial heterogeneity of the soil. But there is very little evidence on how both overstorey structure and soil properties affect the spatial variation of the herb layer. The aim of this study is to evaluate the factors of the soil and overstorey structure by which it is possible to explain the fine-scale variation of herbaceous layer communities in an Eastern European poplar-willow forest. The research was conducted in the “Dnipro-Orils’kiy” Nature Reserve (Ukraine). The research polygon (48°30′51″N, 34°49″02″E) was laid in an Eastern European poplar-willow forest in the floodplain of the River Protich, which is a left inflow of the River Dnipro. The site consists of 7 transects. Each transect was made up of 15 test points. The distance between rows in the site was 3 m. At the site, we established a plot of 45×21 m, with 105 subplots of 3×3 m organized in a regular grid. The adjacent subplots were in close proximity. Vascular plant species lists were recorded at each 3×3 m subplot along with visual estimates of species cover using the nine-degree Braun-Blanquet scale. Within the plot, all woody stems ≥ 1 cm in diameter at breast height were measured and mapped. Dixon’s segregation index was calculated for tree species to quantify their relative spatial mixing. Based on geobotanical descriptions, a phytoindicative assessment of environmental factors according to the Didukh scale was made. The redundancy analysis was used for the analysis of variance in the herbaceous layer species composition. The geographic coordinates of sampling locations were used to generate a set of orthogonal eigenvector-based spatial variables. Two measurements of the overstorey spatial structure were applied: the distances from the nearest tree of each species and the distance based on the evaluation of spatial density of point objects, which are separate trees. In both cases, the distance matrix of sampling locations was calculated, which provided the opportunity to generate eigenvector-based spatial variables. A kernel smoothed intensity function was used to compute the density of the trees’ spatial distribution from the point patterns’ data. Gaussian kernel functions with various bandwidths were used. The coordinates of sampling locations in the space obtained after the conversion of the trees’ spatial distribution densities were used to generate a set of orthogonal eigenvector-based spatial variables, each of them representing a pattern of particular scale within the extent of the bandwidth area structured according to distance and reciprocal placement of the trees. An overall test of random labelling reveals the total nonrandom distribution of the tree stems within the site. The unexplained variation consists of 43.8%. The variation explained solely by soil variables is equal to 15.5%, while the variation explained both by spatial and soil variables is 18.0%. The measure of the overstorey spatial structure, which is based on the evaluation of its density enables us to obtain different estimations depending on the bandwidth. The bandwidth affects the explanatory capacity of the tree stand. A considerable part of the plant community variation explained by soil factors was spatially structured. The orthogonal eigenvector-based spatial variables (dbMEMs) approach can be extended to quantifying the effect of forest structures on the herbaceous layer community. The measure of the overstorey spatial structure, which is based on the evaluation of its density, was very useful in explaining herbaceous layer community variation.

Reconciling the concepts and measures of diversity, rarity and originality in ecology and evolution

The concept of biological diversity, or biodiversity, is at the core of evolutionary and ecological studies. Many indices of biodiversity have been developed in the last four decades, with species being one of the central units of these indices. However, evolutionary and ecological studies need a precise description of species' characteristics to best quantify inter-species diversity, as species are not equivalent and exchangeable. One of the first concepts characterizing species in biodiversity studies was abundance-based rarity. Abundance-based rarity was then complemented by trait- and phylo-based rarity, called species' trait-based and phylogenetic originalities, respectively. Originality, which is a property of an individual species, represents a species' contribution to the overall diversity of a reference set of species. Originality can also be defined as the rarity of a species' characteristics such as the state of a functional trait, which is often assumed to be represented by the position of the species on a phylogenetic tree. We review and compare various approaches for measuring originality, rarity and diversity and demonstrate that (i) even if attempts to bridge these concepts do exist, only a few ecological and evolutionary studies have tried to combine them all in the past two decades; (ii) phylo- and trait-based diversity indices can be written as a function of species rarity and originality measures in several ways; and (iii) there is a need for the joint use of these three types of indices to understand community assembly processes and species' roles in ecosystem functioning in order to protect biodiversity efficiently.

Good neighbors aplenty: fungal endophytes rarely exhibit competitive exclusion patterns across a span of woody habitats

Environmental forces and biotic interactions, both positive and negative, structure ecological communities, but their relative roles remain obscure despite strong theory. For instance, ecologically similar species, based on the principle of limiting similarity, are expected to be most competitive and show negative interactions. Specious communities that assemble along broad environmental gradients afford the most power to test theory, but the communities often are difficult to quantify. Microbes, specifically fungal endophytes of wood, are especially suited for testing community assembly theory because they are relatively easy to sample across a comprehensive range of environmental space with clear axes of variation. Moreover, endophytes mediate key forest carbon cycle processes, and although saprophytic fungi from dead wood typically compete, endophytic fungi in living wood may enhance success through cooperative symbioses. To classify interactions within endophyte communities, we analyzed fungal DNA barcode variation across 22 woody plant species growing in woodlands near Richmond, New South Wales, Australia. We estimated the response of endophytes to the measured wood environment (i.e., 11 anatomical and chemical wood traits) and each other using latent-variable models and identified recurrent communities across wood environments using model-based classification. We used this information to evaluate whether (1) co-occurrence patterns are consistent with strong competitive exclusion, and (2) a priori classifications by trophic mode and phylum distinguish taxa that are more likely to have positive vs. negative associations under the principle of limiting similarity. Fungal endophytes were diverse (mean = 140 taxa/sample), with differences in community composition structured by wood traits. Variation in wood water content and carbon concentration were associated with especially large community shifts. Surprisingly, after accounting for wood traits, fungal species were still more than three times more likely to have positive than negative co-occurrence patterns. That is, patterns consistent with strong competitive exclusion were rare, and positive interactions among fungal endophytes were more common than expected. Confirming the frequency of positive vs. negative interactions among fungal taxa requires experimental tests, and our findings establish clear paths for further study. Evidence to date intriguingly suggests that, across a wide range of wood traits, cooperation may outweigh combat for these fungi.

Experimental dominant plant removal results in contrasting assembly for dominant and non-dominant plants

Understanding why communities appear deterministically dominated by relatively few species is an age-old debate in ecology. We hypothesised that the dominant and non-dominant species in a community are governed by different assembly mechanisms where environmental conditions influence dominant species more than non-dominant species. Further, dominant plants moderate the environment where non-dominant species thrive, diminishing the influence of environmental filtering and increasing the influence of limiting similarity for non-dominant species. We tested these hypotheses by removing two dominant species in five temperate meadows. We found that the composition of the non-dominants diverged while the new dominants converged over time. Phylogenetic analyses suggested that habitat filtering and limiting similarity drove the new dominant species simultaneously. Conversely, non-dominant community assembly appeared more unpredictable. These suggest that dominant species converged towards a predictable environmentally driven optimum, while non-dominant species thrive in a moderated habitat, which probably reduced non-dominant species predictability.

Phenology of Drosophila species across a temperate growing season and implications for behavior

Drosophila community composition is complex in temperate regions with different abundance of flies and species across the growing season. Monitoring Drosophila populations provides insights into the phenology of both native and invasive species. Over a single growing season, we collected Drosophila at regular intervals and determined the number of individuals of the nine species we found in Kansas, USA. Species varied in their presence and abundance through the growing season with peak diversity occurring after the highest seasonal temperatures. We developed models for the abundance of the most common species, Drosophila melanogaster, D. simulans, D. algonquin, and the recent invasive species, D. suzukii. These models revealed that temperature played the largest role in abundance of each species across the season. For the two most commonly studied species, D. melanogaster and D. simulans, the best models indicate shifted thermal optima compared to laboratory studies, implying that fluctuating temperature may play a greater role in the physiology and ecology of these insects than indicated by laboratory studies, and should be considered in global climate change studies.

Flooding and hydrologic connectivity modulate community assembly in a dynamic river-floodplain ecosystem

Braided river floodplains are highly dynamic ecosystems, where aquatic communities are strongly regulated by the hydrologic regime. So far, however, understanding of how flow variation influences assembly mechanisms remains limited. We collected benthic chironomids and oligochaetes over a year across a lateral connectivity gradient in the semi-natural Tagliamento River (Italy). Four bankfull flood events occurred during the study, allowing the assessment of how flooding and hydrologic connectivity mediate the balance between stochastic and deterministic community assembly. While invertebrate density and richness were positively correlated with connectivity, diversity patterns showed no significant correlation. Species turnover through time increased with decreasing connectivity. Contrary to expectations, hydrologic connectivity did not influence the response of community metrics (e.g. diversity, density) to floods. Invertebrate composition was weakly related to connectivity, but changed predictably in response to floods. Multivariate ordinations showed that faunal composition diverged across the waterbodies during stable periods, reflecting differential species sorting across the lateral gradient, but converged again after floods. Stable hydrological periods allowed communities to assemble deterministically with prevalence of non-random beta-diversity and co-occurrence patterns and larger proportion of compositional variation explained by local abiotic features. These signals of deterministic processes declined after flooding events. This occurred despite no apparent evidence of flood-induced homogenisation of habitat conditions. This study is among the first to examine the annual dynamic of aquatic assemblages across a hydrologic connectivity gradient in a natural floodplain. Results highlight how biodiversity can exhibit complex relations with hydrologic connectivity. However, appraisal of the assembly mechanisms through time indicated that flooding shifted the balance from deterministic species sorting across floodplain habitats, towards stochastic processes related to organisms redistribution and the likely resetting of assembly to earlier stages.

Phylogenetic Community Structure and Niche Differentiation in Termites of the Tropical Dry Forests of Colombia

The mechanisms that structure species communities are still debated. We addressed this question for termite assemblages from tropical dry forests in Colombia. These forests are endangered and poorly understood ecosystems and termites are important ecosystem engineers in the tropics. Using biodiversity and environmental data, combined with phylogenetic community analyses, trait mapping, and stable isotopes studies, we investigated the termite community composition of three protected dry forests in Colombia. Our data suggest that the structuring mechanisms differed between sites. Phylogenetic overdispersion of termite assemblages correlated with decreasing rainfall and elevation and increasing temperature. Food niche traits-classified as feeding groups and quantified by δ15N‰ and δ13C‰ isotope signatures-were phylogenetically conserved. Hence, the overdispersion pattern implies increasing interspecific competition with decreasing drier and warmer conditions, which is also supported by fewer species occurring at the driest site. Our results are in line with a hypothesis that decreased biomass production limits resource availability for termites, which leads to competition. Along with this comes a diet shift: termites from drier plots had higher δ13C signatures, reflecting higher δ13C values in the litter and more C4 plants. Our study shows how a phylogenetic community approach combined with trait analyses can contribute to gaining the first insights into mechanisms structuring whole termite assemblages.

Key colonist pools and habitat filters mediate the composition of fiddler crab-associated bacterial communities

The diversity and composition of local communities depends strongly on the pool of species that have been able to colonize that community from elsewhere. Typically this is thought to depend on a larger regional species pool that is subject to local environmental constraints that act as "filters." Often, however, colonists arrive from multiple sources that differ in habitat conditions and have therefore already experienced distinct "prefiltering." Consequently, it is the interaction of species from these distinct pools that determine the composition of local communities. This interaction is particularly important when certain colonist pools provide keystone species with disproportionate roles on community assembly. We propose to identify these key colonist pools and their interaction with local habitat filters by quantifying community-level responses to colonist pool manipulation. We tested this framework to assess the contribution of surface and burrow sediment bacteria to bacterial communities associated with the fiddler crab, Uca panacea. In a mesocosm experiment, we combined normal and autoclaved surface and burrow sediment in a factorial experimental design, and we evaluated the community-level responses of carapace and gut microbial assemblages to sediment treatments with next-generation sequencing of the 16S rRNA gene. Results from carapace bacterial communities indicate that burrow sediments contribute most recruits, but surface sediments provide a few key colonizers that become established in the carapace community. In contrast, the composition of gut-associated microbial communities responded only to surface bacteria manipulation, despite being highly dissimilar from the community composition in both the surface and burrow source pools. These results suggest that assembly in the gut depends primarily on colonization from the surface sediment and regulation by habitat filtering. For fiddler crab-associated bacteria, we can conclude that key colonist pools and habitat filters regulate the influence of multiple colonist pools. Incorporating and distinguishing the contribution of multiple sources of species, rather than a single regional species pool, may better explain community dynamics in many systems, especially those with weak habitat filters.

An ordination approach to explore similarities among communities

Analysis of similarities among communities can help to decipher the biogeographical, evolutionary, and ecological factors that drive local diversity. Recent indices of similarity among communities incorporate not only information on species presence and abundance but also information on how similar species are in their traits and how closely related they are in terms of taxonomy or phylogeny. Towards this aim, trait-based, taxonomic or phylogenetic similarities among species have been defined and bounded between 0 (species are maximally distinct) and 1 (species are similar). A required property for an index of similarity between two communities is that it must provide minimum similarity (0) where communities have maximally distinct species, as well as maximum similarity (1) where communities are equivalent in their trait, taxonomic or phylogenetic compositions. Here, I developed a new ordination methodology that conforms to the requirement: double similarity principal component analysis (DSPCA). DSPCA summarizes multidimensional trait-based, taxonomic or phylogenetic similarities among communities into orthogonal axes. The species that drive each similarity pattern can be identified together with their traits or with their taxonomic or phylogenetic positions. I applied this methodology to theoretical examples and to empirical data sets on bird and bat communities to illustrate key properties of DSPCA. I compared the results obtained with DSPCA with those provided by related approaches. Theoretical and empirical case studies highlight the following additional properties of DSPCA: (i) axes are orthogonal and identify independent (dis)similarity patterns between communities; (ii) the more functionally, taxonomically or phylogenetically similar communities are, the closer they are on an axis; (iii) the coordinate of a species on an axis expresses how representative the species is of the pattern identified by the axis; and (iv) a species is representative of x communities if the functional, taxonomic or phylogenetic characteristics of this species are very common within each of these x communities. DSPCA is an efficient approach to visualize functional, taxonomic and phylogenetic similarities between communities. It is also a useful alternative to recent methods dedicated to phylogenetic diversity patterns. It will be an asset for all studies that aim to compare functional, taxonomic, genetic and phylogenetic diversity.

Traditional plant functional groups explain variation in economic but not size-related traits across the tundra biome

AIM

Plant functional groups are widely used in community ecology and earth system modelling to describe trait variation within and across plant communities. However, this approach rests on the assumption that functional groups explain a large proportion of trait variation among species. We test whether four commonly used plant functional groups represent variation in six ecologically important plant traits.

LOCATION

Tundra biome.

TIME PERIOD

Data collected between 1964 and 2016.

MAJOR TAXA STUDIED

295 tundra vascular plant species.

METHODS

We compiled a database of six plant traits (plant height, leaf area, specific leaf area, leaf dry matter content, leaf nitrogen, seed mass) for tundra species. We examined the variation in species-level trait expression explained by four traditional functional groups (evergreen shrubs, deciduous shrubs, graminoids, forbs), and whether variation explained was dependent upon the traits included in analysis. We further compared the explanatory power and species composition of functional groups to alternative classifications generated using post hoc clustering of species-level traits.

RESULTS

Traditional functional groups explained significant differences in trait expression, particularly amongst traits associated with resource economics, which were consistent across sites and at the biome scale. However, functional groups explained 19% of overall trait variation and poorly represented differences in traits associated with plant size. Post hoc classification of species did not correspond well with traditional functional groups, and explained twice as much variation in species-level trait expression.

MAIN CONCLUSIONS

Traditional functional groups only coarsely represent variation in well-measured traits within tundra plant communities, and better explain resource economic traits than size-related traits. We recommend caution when using functional group approaches to predict tundra vegetation change, or ecosystem functions relating to plant size, such as albedo or carbon storage. We argue that alternative classifications or direct use of specific plant traits could provide new insights for ecological prediction and modelling.

Flower-visitor communities of an arcto-alpine plant-Global patterns in species richness, phylogenetic diversity and ecological functioning

Pollination is an ecosystem function of global importance. Yet, who visits the flower of specific plants, how the composition of these visitors varies in space and time and how such variation translates into pollination services are hard to establish. The use of DNA barcodes allows us to address ecological patterns involving thousands of taxa that are difficult to identify. To clarify the regional variation in the visitor community of a widespread flower resource, we compared the composition of the arthropod community visiting species in the genus Dryas (mountain avens, family Rosaceae), throughout Arctic and high-alpine areas. At each of 15 sites, we sampled Dryas visitors with 100 sticky flower mimics and identified specimens to Barcode Index Numbers (BINs) using a partial sequence of the mitochondrial COI gene. As a measure of ecosystem functioning, we quantified variation in the seed set of Dryas. To test for an association between phylogenetic and functional diversity, we characterized the structure of local visitor communities with both taxonomic and phylogenetic descriptors. In total, we detected 1,360 different BINs, dominated by Diptera and Hymenoptera. The richness of visitors at each site appeared to be driven by local temperature and precipitation. Phylogeographic structure seemed reflective of geological history and mirrored trans-Arctic patterns detected in plants. Seed set success varied widely among sites, with little variation attributable to pollinator species richness. This pattern suggests idiosyncratic associations, with function dominated by few and potentially different taxa at each site. Taken together, our findings illustrate the role of post-glacial history in the assembly of flower-visitor communities in the Arctic and offer insights for understanding how diversity translates into ecosystem functioning.

Do all roads lead to Rome? Exploring community trajectories in response to anthropogenic salinization and dilution of rivers

Abiotic stress shapes how communities assemble and support ecological functions. However, it remains unclear whether artificially increasing or decreasing stress levels would lead to communities assembling predictably along a single axis of variation or along multiple context-dependent trajectories of change. In response to stress intensity alterations, we hypothesize that a single trajectory of change occurs when trait-based assembly prevails, while multiple trajectories of change arise when dispersal-related processes modify colonization and trait-filtering dynamics. Here, we tested these hypotheses using aquatic macroinvertebrates from rivers exposed to gradients of natural salinity and artificially diluted or salinized ion contents. Our results showed that trait-filtering was important in driving community assembly in natural and diluted rivers, while dispersal-related processes seemed to play a relevant role in response to salinization. Salinized rivers showed novel communities with different trait composition, while natural and diluted communities exhibited similar taxonomic and trait compositional patterns along the conductivity gradient. Our findings suggest that the artificial modification of chemical stressors can result in different biological communities, depending on the direction of the change (salinization or dilution), with trait-filtering, and organism dispersal and colonization dynamics having differential roles in community assembly. The approach presented here provides both empirical and conceptual insights that can help in anticipating the ecological effects of global change, especially for those stressors with both natural and anthropogenic origins.This article is part of the theme issue 'Salt in freshwaters: causes, ecological consequences and future prospects'.

Environment and past land use together predict functional diversity in a temperate forest

Environment and human land use both shape forest composition. Abiotic conditions sift tree species from a regional pool via functional traits that influence species' suitability to the local environment. In addition, human land use can modify species distributions and change functional diversity of forests. However, it is unclear how environment and land use simultaneously shape functional diversity of tree communities. Land-use legacies are especially prominent in temperate forest landscapes that have been extensively modified by humans in the last few centuries. Across a 900-ha temperate deciduous forest in the northeastern United States, comprising a mosaic of different-aged stands due to past human land use, we used four key functional traits-maximum height, rooting depth, wood density, and seed mass-to examine how multiple environmental and land-use variables influenced species distributions and functional diversity. We sampled ~40,000 trees >8 cm DBH within 485 plots totaling 137 ha. Species within plots were more functionally similar than expected by chance when we estimated functional diversity using all traits together (multi-trait), and to a lesser degree, with each trait separately. Multi-trait functional diversity was most strongly correlated with distance from the perennial stream, elevation, slope, and forest age. Environmental and land-use predictors varied in their correlation with functional diversities of the four individual traits. Landscape-wide change in abundances of individual species also correlated with both environment and land-use variables, but magnitudes of trait-environment interactions were generally stronger than trait interactions with land use. These findings can be applied for restoration and assisted regeneration of human-modified temperate forests by using traits to predict which tree species would establish well in relation to land-use history, topography, and soil conditions.

Plant Attributes that Drive Dispersal and Establishment Limitation in Tropical Agricultural Landscapes

Factors that influence tropical-forest regeneration have been of interest across the tropics. We tested the degree of dispersal and establishment limitation of pioneer and non-pioneer tree species with different dispersal modes and seed sizes, using data on both seed fall and seedling establishment in primary forest, secondary forest, and pasture excluded from livestock. The study took place in a lowland tropical rain forest in southeastern Mexico. To calculate dispersal and establishment limitation, we used a density-weighted index that considers: (1) whether a seed or seedling of a given species has arrived in the sample area; and (2) the fraction of seeds or seedlings contributed by a given species relative to the total number of seeds or seedlings arriving at a sampling station. Dispersal limitation of non-pioneer species and animal-dispersed species decreased with succession. The secondary forest had less dispersal limitation for wind-dispersed pioneers than pasture, resulting in a dense aggregation of species with seeds dispersed by wind. Overall, establishment limitation differed between animal-dispersed and wind-dispersed species in the primary forest, and was negatively correlated with seed size. The low capacity of most species to arrive, germinate, and establish as seedlings in pastures slows succession back to forest. To overcome barriers to natural succession in pastures, transplanting seedlings of non-pioneer species is suggested because most of them show high dispersal and establishment limitation.

Integrating Genetic and Demographic Effects of Connectivity on Population Stability: The Case of Hatchery Trucking in Salmon

Connectivity among populations can have counteracting effects on population stability. Demographically, connectivity can rescue local populations but increase the synchrony across populations. Genetically, connectivity can counteract drift locally but homogenize genotypes across populations. Population independence and diversity underlies system-level buffering against environmental variability, termed the portfolio effect. The portfolio effect has declined in California fall-run Chinook salmon, possibly in part because of the trucking of juvenile hatchery-reared fish for downstream release, which reduces juvenile mortality but increases the connectivity between rivers. We use a dynamical population model to test whether this increased connectivity can explain the loss of the portfolio effect and quantify the relative demographic and genetic contributions to portfolio effect erosion. In the model, populations experience different within-population environmental conditions and the same time-variable ocean conditions, the response to which can depend on a quantitative genetic trait. We find that increased trucking for one population's hatchery can lead to a loss of the portfolio effect, with a system-level trade-off between increased average abundance and increased variability in abundance. This trade-off is much stronger when we include the effects of genetic homogenization than when we consider demographic synchronization alone. Therefore, genetic homogenization can outweigh demographic synchrony in determining the system-level effect of connectivity.

Using co-occurrence information and trait composition to understand individual plant performance in grassland communities

Depending on the strength of environmental filtering and competitive exclusion, successful colonizers of plant communities show varying degrees of similarity to resident species with respect to functional traits. For the present study, colonizer's performance was assessed in relation to the degree of fit with the resident community, and in addition, in relation to the community's trait profile and the environmental factors at the study locations. The two-year field experiment investigated the relative growth rates of 130 species that had been transplanted into German grassland communities varying in intensities of land-use. The transplanted species were selected in accordance with the following scenarios: species with highly similar or dissimilar traits to residents, species with highest degree of co-occurrence with resident species and species chosen randomly from the local species pool. The performance of transplanted phytometers depended on the scenario according to which the species were selected, on community trait diversity, and in addition, often on the interaction of both and on land use intensity. The total amount of explained variance in performance was low, but increased considerably when species identity was taken into account. In general, individuals in the co-occurrence scenario performed better than those selected based on trait information or those selected randomly. Different predictors were important in different seasons, demonstrating a limited temporal validity of performance models.

A synthesis of ecological and evolutionary determinants of bat diversity across spatial scales

Background

Diversity patterns result from ecological to evolutionary processes operating at different spatial and temporal scales. Species trait variation determine the spatial scales at which organisms perceive the environment. Despite this knowledge, the coupling of all these factors to understand how diversity is structured is still deficient. Here, we review the role of ecological and evolutionary processes operating across different hierarchically spatial scales to shape diversity patterns of bats—the second largest mammal order and the only mammals with real flight capability.

Main body

We observed that flight development and its provision of increased dispersal ability influenced the diversification, life history, geographic distribution, and local interspecific interactions of bats, differently across multiple spatial scales. Niche packing combined with different flight, foraging and echolocation strategies and differential use of air space allowed the coexistence among bats as well as for an increased diversity supported by the environment. Considering distinct bat species distributions across space due to their functional characteristics, we assert that understanding such characteristics in Chiroptera improves the knowledge on ecological processes at different scales. We also point two main knowledge gaps that limit progress on the knowledge on scale-dependence of ecological and evolutionary processes in bats: a geographical bias, showing that research on bats is mainly done in the New World; and the lack of studies addressing the mesoscale (i.e. landscape and metacommunity scales).

Conclusions

We propose that it is essential to couple spatial scales and different zoogeographical regions along with their functional traits, to address bat diversity patterns and understand how they are distributed across the environment. Understanding how bats perceive space is a complex task: all bats can fly, but their perception of space varies with their biological traits.

Electronic supplementary material

The online version of this article (10.1186/s12898-018-0174-z) contains supplementary material, which is available to authorized users.

Processes and patterns of interaction as units of selection: An introduction to ITSNTS thinking

Many practicing biologists accept that nothing in their discipline makes sense except in the light of evolution, and that natural selection is evolution's principal sense-maker. But what natural selection actually is (a force or a statistical outcome, for example) and the levels of the biological hierarchy (genes, organisms, species, or even ecosystems) at which it operates directly are still actively disputed among philosophers and theoretical biologists. Most formulations of evolution by natural selection emphasize the differential reproduction of entities at one or the other of these levels. Some also recognize differential persistence, but in either case the focus is on lineages of material things: even species can be thought of as spatiotemporally restricted, if dispersed, physical beings. Few consider-as "units of selection" in their own right-the processes implemented by genes, cells, species, or communities. "It's the song not the singer" (ITSNTS) theory does that, also claiming that evolution by natural selection of processes is more easily understood and explained as differential persistence than as differential reproduction. ITSNTS was formulated as a response to the observation that the collective functions of microbial communities (the songs) are more stably conserved and ecologically relevant than are the taxa that implement them (the singers). It aims to serve as a useful corrective to claims that "holobionts" (microbes and their animal or plant hosts) are aggregate "units of selection," claims that often conflate meanings of that latter term. But ITSNS also seems broadly applicable, for example, to the evolution of global biogeochemical cycles and the definition of ecosystem function.

Community Assembly Theory as a Framework for Biological Invasions

Biological invasions present a global problem underlain by an ecological paradox that thwarts explanation: how do some exotic species, evolutionarily naïve to their new environments, outperform locally adapted natives? We propose that community assembly theory provides a framework for addressing this question. Local community assembly rules can be defined by evaluating how native species' traits interact with community filters to affect species abundance. Evaluation of exotic species against this benchmark indicates that exotics that follow assembly rules behave like natives, while those exhibiting novel interactions with community filters can greatly underperform or outperform natives. Additionally, advantages gained by exotics over natives following disturbance can be explained by accounting for extrinsic assembly processes that bias exotic traits toward ruderal strategies.

Long-term nitrogen addition affects the phylogenetic turnover of soil microbial community responding to moisture pulse

How press disturbance (long-term) influences the phylogenetic turnover of soil microbial communities responding to pulse disturbances (short-term) is not fully known. Understanding the complex connections between the history of environmental conditions, assembly processes and microbial community dynamics is necessary to predict microbial response to perturbation. We started by investigating phylogenetic spatial turnover (based on DNA) of soil prokaryotic communities after long-term nitrogen (N) deposition and temporal turnover (based on RNA) of communities responding to pulse by conducting short-term rewetting experiments. The results showed that moderate N addition increased ecological stochasticity and phylogenetic diversity. In contrast, high N addition slightly increased homogeneous selection and decreased phylogenetic diversity. Examining the system with higher phylogenetic resolution revealed a moderate contribution of variable selection across the whole N gradient. The moisture pulse experiment showed that high N soils had higher rates of phylogenetic turnover across short phylogenetic distances and significant changes in community compositions through time. Long-term N input history influenced spatial turnover of microbial communities, but the dominant community assembly mechanisms differed across different N deposition gradients. We further revealed an interaction between press and pulse disturbances whereby deterministic processes were particularly important following pulse disturbances in high N soils.

Analysing taxonomic structures and local ecological processes in temperate forests in North Eastern China

BACKGROUND

One of the core issues of forest community ecology is the exploration of how ecological processes affect community structure. The relative importance of different processes is still under debate. This study addresses four questions: (1) how is the taxonomic structure of a forest community affected by spatial scale? (2) does the taxonomic structure reveal effects of local processes such as environmental filtering, dispersal limitation or interspecific competition at a local scale? (3) does the effect of local processes on the taxonomic structure vary with the spatial scale? (4) does the analysis based on taxonomic structures provide similar insights when compared with the use of phylogenetic information? Based on the data collected in two large forest observational field studies, the taxonomic structures of the plant communities were analyzed at different sampling scales using taxonomic ratios (number of genera/number of species, number of families/number of species), and the relationship between the number of higher taxa and the number of species. Two random null models were used and the "standardized effect size" (SES) of taxonomic ratios was calculated, to assess possible differences between the observed and simulated taxonomic structures, which may be caused by specific ecological processes. We further applied a phylogeny-based method to compare results with those of the taxonomic approach.

RESULTS

As expected, the taxonomic ratios decline with increasing grain size. The quantitative relationship between genera/families and species, described by a linearized power function, showed a good fit. With the exception of the family-species relationship in the Jiaohe study area, the exponents of the genus/family-species relationships did not show any scale dependent effects. The taxonomic ratios of the observed communities had significantly lower values than those of the simulated random community under the test of two null models at almost all scales. Null Model 2 which considered the spatial dispersion of species generated a taxonomic structure which proved to be more consistent with that in the observed community. As sampling sizes increased from 20 m × 20 m to 50 m × 50 m, the magnitudes of SESs of taxonomic ratios increased. Based on the phylogenetic analysis, we found that the Jiaohe plot was phylogenetically clustered at almost all scales. We detected significant phylogenetically overdispersion at the 20 m × 20 m and 30 m × 30 m scales in the Liangshui plot.

CONCLUSIONS

The results suggest that the effect of abiotic filtering is greater than the effects of interspecific competition in shaping the local community at almost all scales. Local processes influence the taxonomic structures, but their combined effects vary with the spatial scale. The taxonomic approach provides similar insights as the phylogenetic approach, especially when we applied a more conservative null model. Analysing taxonomic structure may be a useful tool for communities where well-resolved phylogenetic data are not available.

Biodiversity and ecosystem functioning in dynamic landscapes

The relationship between biodiversity and ecosystem functioning (BEF) and its consequence for ecosystem services has predominantly been studied by controlled, short-term and small-scale experiments under standardized environmental conditions and constant community compositions. However, changes in biodiversity occur in real-world ecosystems with varying environments and a dynamic community composition. In this theme issue, we present novel research on BEF in such dynamic communities. The contributions are organized in three sections on BEF relationships in (i) multi-trophic diversity, (ii) non-equilibrium biodiversity under disturbance and varying environmental conditions, and (iii) large spatial and long temporal scales. The first section shows that multi-trophic BEF relationships often appear idiosyncratic, while accounting for species traits enables a predictive understanding. Future BEF research on complex communities needs to include ecological theory that is based on first principles of species-averaged body masses, stoichiometry and effects of environmental conditions such as temperature. The second section illustrates that disturbance and varying environments have direct as well as indirect (via changes in species richness, community composition and species' traits) effects on BEF relationships. Fluctuations in biodiversity (species richness, community composition and also trait dominance within species) can severely modify BEF relationships. The third section demonstrates that BEF at larger spatial scales is driven by different variables. While species richness per se and community biomass are most important, species identity effects and community composition are less important than at small scales. Across long temporal scales, mass extinctions represent severe changes in biodiversity with mixed effects on ecosystem functions. Together, the contributions of this theme issue identify new research frontiers and answer some open questions on BEF relationships in dynamic communities of real-world landscapes.

Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth

Background: The phyllosphere hosts a variety of microorganisms, including bacteria, which can play a positive role in the success of the host plant. Bacterial communities in the phylloplane are influenced by both biotic and abiotic factors, including host plant surface topography and chemistry, which change in concert with microbial communities as the plant leaves develop and age.

Methods: We examined how the Zea mays L. leaf microbial community structure changed with plant age. Ribosomal spacer length and scanning electron microscopic imaging strategies were used to assess microbial community composition across maize plant ages, using a novel staggered experimental design.

Results: Significant changes in community composition were observed for both molecular and imaging analyses, and the two analysis methods provided complementary information about bacterial community structure within each leaf developmental stage.

Conclusions: Both taxonomic and cell-size trait patterns provided evidence for niche-based contributions to microbial community development on leaves.

Drivers of community assembly in tropical forest restoration sites: role of local environment, landscape, and space

There is increasing recognition that community assembly theory can offer valuable insights for ecological restoration. We studied community assembly processes following tropical forest restoration efforts, using dung beetles (Scarabaeinae) as a focal taxon to investigate taxonomic and functional patterns of biodiversity recovery. We evaluated the relative importance of the local environment (i.e., canopy cover, understory cover, tree basal area, and soil texture), landscape context (i.e., habitat patch proximity and availability and percentage of surrounding area classified as natural forest or Eucalyptus spp. plantation), and space (i.e., spatial proximity of the study areas to estimate dispersal limitation or unmeasured spatially structured processes) on dung beetle species and functional trait composition across a gradient of 15 restoration sites in Brazilian Atlantic Forest. We also assessed which factors were the primary determinants in the establishment of individual dung beetle functional groups, classified according to size, food relocation habit, diet, and period of flight activity. Both species and functional trait composition were most strongly influenced by the local environment, indicating that assembly was predominantly driven by niche-based processes. Most of the variation explained by space was co-explained by local environment and landscape context, ruling out a strong influence of dispersal limitation and random colonization on assembly following restoration. In addition, nearly all of the variance explained by landscape context was co-explained by local environment, suggesting that arrival and establishment at a site depends on both local and landscape-scale environmental factors. Despite strong evidence for niche-based assembly, a large amount of variation remained unexplained in all models, suggesting that stochastic processes and/or unmeasured environmental variables also play an important role. The relative importance of local environment, landscape context, and space changed considerably when analyzing the assembly mechanisms of each functional group separately. Therefore, to recover distinct functional traits in restoration sites, it may be necessary to manipulate different components of the local environment and surrounding landscape. Overall, this study shows that assembly rules can help to better understand recovery processes, enabling improvement of future restoration efforts.

Predicting vegetation type through physiological and environmental interactions with leaf traits: evergreen and deciduous forests in an earth system modeling framework

Earth system models are incorporating plant trait diversity into their land components to better predict vegetation dynamics in a changing climate. However, extant plant trait distributions will not allow extrapolations to novel community assemblages in future climates, which will require a mechanistic understanding of the trade-offs that determine trait diversity. In this study, we show how physiological trade-offs involving leaf mass per unit area (LMA), leaf lifespan, leaf nitrogen, and leaf respiration may explain the distribution patterns of evergreen and deciduous trees in the temperate and boreal zones based on (1) an evolutionary analysis of a simple mathematical model and (2) simulation experiments of an individual-based dynamic vegetation model (i.e., LM3-PPA). The evolutionary analysis shows that these leaf traits set up a trade-off between carbon- and nitrogen-use efficiency at the scale of individual trees and therefore determine competitively dominant leaf strategies. As soil nitrogen availability increases, the dominant leaf strategy switches from one that is high in nitrogen-use efficiency to one that is high in carbon-use efficiency or, equivalently, from high-LMA/long-lived leaves (i.e., evergreen) to low-LMA/short-lived leaves (i.e., deciduous). In a region of intermediate soil nitrogen availability, the dominant leaf strategy may be either deciduous or evergreen depending on the initial conditions of plant trait abundance (i.e., founder controlled) due to feedbacks of leaf traits on soil nitrogen mineralization through litter quality. Simulated successional patterns by LM3-PPA from the leaf physiological trade-offs are consistent with observed successional dynamics of evergreen and deciduous forests at three sites spanning the temperate to boreal zones.