Trait-based ecology, trait-free ecology, and in between.

Trait-based ecology has become a popular phrase. But all species have traits, and their contributions to ecological processes are governed by those traits. So then, is not all ecology trait-based? Actually, there do exist areas of ecology that are consciously trait-free, such as neutral theory and species abundance distributions. But much of ecology could be considered actually or potentially trait-based. A spectrum is described, from trait-free through trait-implicit and trait-explicit to trait-centric. Trait-centric ecology includes positioning ecological strategies along trait dimensions, with a view to inferring commonalities and to generalizing from species studied in more detail. Trait-explicit includes physiological and functional ecology, and areas of community ecology and ecosystem function that invoke traits. Trait-implicit topics are those where it is important that species are different, but formulations did not initially characterize the differences via traits. Subsequently, strands within these trait-implicit topics have often moved towards making use of species traits, so the boundary with trait-explicit is permeable. Trait-based ecology is productive because of the dialogue between understanding processes in detail, via traits that relate most closely, and generalizing across many species, via traits that can be compared widely. An enduring key question for trait-based ecology is which traits for which processes.

Symbiont plasticity as a driver of plant success.

We discuss which plant species are likely to become winners, that is achieve the highest global abundance, in changing landscapes, and whether plant-associated microbes play a determining role. Reduction and fragmentation of natural habitats in historic landscapes have led to the emergence of patchy, hybrid landscapes, and novel landscapes where anthropogenic ecosystems prevail. In patchy landscapes, species with broad niches are favoured. Plasticity in the degree of association with symbiotic microbes may contribute to broader plant niches and optimization of symbiosis costs and benefits, by downregulating symbiosis when it is unnecessary and upregulating it when it is beneficial. Plasticity can also be expressed as the switch from one type of mutualism to another, for example from nutritive to defensive mutualism with increasing soil fertility and the associated increase in parasite load. Upon dispersal, wide mutualistic partner receptivity is another facet of symbiont plasticity that becomes beneficial, because plants are not limited by the availability of specialist partners when arriving at new locations. Thus, under conditions of global change, symbiont plasticity allows plants to optimize the activity of mutualistic relationships, potentially allowing them to become winners by maximizing geographic occupancy and local abundance.

Substituting space for time: Bird responses to forest loss in space provide a general picture of responses over time.

The practice of space-for-time substitution assumes that the responses of species or communities to land-use change over space represents how they will respond to that same change over time. Space-for-time substitution is commonly used in both ecology and conservation, but whether the assumption produces reliable insights remains inconclusive. Here, we tested space-for-time substitution using data from the North American Breeding Bird Survey (BBS) and Global Forest Change (GFC) to compare the effects of landscape-scale forest cover on bird richness and abundance over time and space, for 25 space-time comparisons. Each comparison consisted of a landscape that experienced at least 20% forest loss over 19 years (temporal site) and a set of 15-19 landscapes (spatial sites) that represented the same forest cover gradient over space in 2019 as experienced over time in their corresponding temporal site. Across the 25 comparisons, the observed responses of forest and open-habitat birds to forest cover over time generally aligned with their responses to forest cover over space, but with comparatively higher variability in the magnitude and direction of effect across the 25 temporal slopes than across the 25 spatial slopes. On average, the mean differences between the spatial and temporal slopes across the 25 space-time comparisons frequently overlapped with zero, suggesting that the spatial slopes are generally informative of the temporal slopes. However, we observed high variability around these mean differences, indicating that a single spatial slope is not strongly predictive of its corresponding temporal slope. We suggest that our results may be explained by annual variability in other relevant environmental factors that combine to produce complex effects on population abundances over time that are not easily captured by snapshots in space. While not being a 1:1 proxy, measuring bird responses to changes in habitat amount in space provides an idea on how birds might be expected to eventually equilibrate to similar changes in habitat amount over time. Further, analyses such as this could be potentially used to screen for cases of regional space-time mismatches where population-limiting factors other than habitat could be playing a more important role in the population trends observed there.

Assessing the sensitivity and resistance of communities in a changing environment.

We propose that the ecological resilience of communities to permanent changes of the environment can be based on how variation in the overall abundance of individuals affects the number of species. Community sensitivity is defined as the ratio between the rate of change in the log expected number of species and the rate of change in the log expected number of individuals in the community. High community sensitivity means that small changes in the total abundance strongly impact the number of species. Community resistance is the proportional reduction in expected number of individuals that the community can sustain before expecting to lose one species. A small value of community resistance means that the community can only endure a small reduction in abundance before it is expected to lose one species. Based on long-term studies of four bird communities in European deciduous forests at different latitudes large differences were found in the resilience to environmental perturbations. Estimating the variance components of the species abundance distribution revealed how different processes contributed to the community sensitivity and resistance. Species heterogeneity in the population dynamics was the largest component, but its proportion varied among communities. Species-specific response to environmental fluctuations was the second major component of the variation in abundance. Estimates of community sensitivity and resistance based on data only from a single year were in general larger than those based on estimates from longer time series. Thus, our approach can provide rapid and conservative assessment of the resilience of communities to environmental changes also including only short-term data. This study shows that a general ecological mechanism, caused by increased strength of density dependence due to reduction in resource availability, can provide an intuitive measure of community resilience to environmental variation. Our analyses also illustrate the importance of including specific assumptions about how different processes affect community dynamics. For example, if stochastic fluctuations in the environment affect all species in a similar way, the sensitivity and resistance of the community to environmental changes will be different from communities in which all species show independent responses.

Quantitative and dynamic profiling of human gut core microbiota by real-time PCR.

The human gut microbiota refers to a diverse community of microorganisms that symbiotically exist in the human intestinal system. Altered microbial communities have been linked to many human pathologies. However, there is a lack of rapid and efficient methods to assess gut microbiota signatures in practice. To address this, we established an appraisal system containing 45 quantitative real-time polymerase chain reaction (qPCR) assays targeting gut core microbes with high prevalence and/or abundance in the population. Through comparative genomic analysis, we selected novel species-specific genetic markers and primers for 31 of the 45 core microbes with no previously reported specific primers or whose primers needed improvement in specificity. We comprehensively evaluated the performance of the qPCR assays and demonstrated that they showed good sensitivity, selectivity, and quantitative linearity for each target. The limit of detection ranged from 0.1 to 1.0 pg/µL for the genomic DNA of these targets. We also demonstrated the high consistency (Pearson's r = 0.8688, P < 0.0001) between the qPCR method and metagenomics next-generation sequencing (mNGS) method in analyzing the abundance of selected bacteria in 22 human fecal samples. Moreover, we quantified the dynamic changes (over 8 weeks) of these core microbes in 14 individuals using qPCR, and considerable stability was demonstrated in most participants, albeit with significant individual differences. Overall, this study enables the simple and rapid quantification of 45 core microbes in the human gut, providing a promising tool to understand the role of gut core microbiota in human health and disease. KEY POINTS: • A panel of original qPCR assays was developed to quantify human gut core microbes. • The qPCR assays were evaluated and compared with mNGS using real fecal samples. • This method was used to dynamically profile the gut core microbiota in individuals.

How do species richness and its component dependence vary along the natural restoration in extremely heterogeneous forest ecosystems?

Giant habitat heterogeneity is an important factor contributing to the high species richness (SR) in karst forests. Yet, the driving factor behind the alterations in SR patterns during natural restoration remains unclear. In this study, we established the forest dynamics plots along the natural restoration sequence (including shrub-tree mixed forest stage (SC), secondary forest stage (SG) and old-growth forest sage (OG)) in degraded karst forests to compare the SR and the dependence on its components (including total community abundance, species abundance distribution (SAD), and conspecific spatial aggregation (CSA)) among stages of natural restoration. By evaluating the degree of contribution of the components to local SR and rarefied SR, we found that the SG exhibited the highest local SR, while the rarefied SR remained increasing along the restoration sequence after controlling the sample size. At SC-SG stage, SAD and CSA contributed negatively to the differences in SR, while abundance made a positive contribution to SR differences. At SG-OG, abundance contributed positively to the difference in SR at all scales, while SAD contributed negatively at small scales. No significant contribution of CSA was found at observed scales. In addition, local SR varied more significantly with PIE than with abundance. Our research emphasizes the importance of eliminating the influence of abundance on species richness in forest ecology and management, as well as the significance of separately evaluating the components that shape the diversity patterns.

Temporal change in functional rarity in marine fish assemblages.

Recent research has uncovered rapid compositional and structural reorganization of ecological assemblages, with these changes particularly evident in marine ecosystems. However, the extent to which these ongoing changes in taxonomic diversity are a proxy for change in functional diversity is not well understood. Here we focus on trends in rarity to ask how taxonomic rarity and functional rarity covary over time. Our analysis, drawing on 30 years of scientific trawl data, reveals that the direction of temporal shifts in taxonomic rarity in two Scottish marine ecosystems is consistent with a null model of change in assemblage size (i.e. change in numbers of species and/or individuals). In both cases, however, functional rarity increases, as assemblages become larger, rather than showing the expected decrease. These results underline the importance of measuring both taxonomic and functional dimensions of diversity when assessing and interpreting biodiversity change.

Land use diversification may mitigate on-site land use impacts on mammal populations and assemblages.

Land use is a major cause of biodiversity decline worldwide. Agricultural and forestry diversification measures, such as the inclusion of natural elements or diversified crop types, may reduce impacts on biodiversity. However, the extent to which such measures may compensate for the negative impacts of land use remains unknown. To fill that gap, we synthesised data from 99 studies that recorded mammal populations or assemblages in natural reference sites and in cropland and forest plantations, with or without diversification measures. We quantified the responses to diversification measures based on individual species abundance, species richness and assemblage intactness as quantified by the mean species abundance indicator. In cropland with natural elements, mammal species abundance and richness were, on average, similar to natural conditions, while in cropland without natural elements they were reduced by 28% and 34%, respectively. We found that mammal species richness was comparable between diversified forest plantations and natural reference sites, and 32% lower in plantations without natural elements. In both cropland and plantations, assemblage intactness was reduced compared with natural reference conditions, but the reduction was smaller if diversification measures were in place. In addition, we found that responses to land use were modified by species traits and environmental context. While habitat specialist populations were reduced in cropland without diversification and in forest plantations, habitat generalists benefited. Furthermore, assemblages were impacted more by land use in tropical regions and landscapes containing a larger share of (semi)natural habitat compared with temperate regions and more converted landscapes. Given that mammal assemblage intactness is reduced also when diversification measures are in place, special attention should be directed to species that suffer from land use impacts. That said, our results suggest potential for reconciling land use and mammal conservation, provided that the diversification measures do not compromise yield.

Offshore Wind Energy and Marine Biodiversity in the North Sea: Life Cycle Impact Assessment for Benthic Communities.

Large-scale offshore wind energy developments represent a major player in the energy transition but are likely to have (negative or positive) impacts on marine biodiversity. Wind turbine foundations and sour protection often replace soft sediment with hard substrates, creating artificial reefs for sessile dwellers. Offshore wind farm (OWF) furthermore leads to a decrease in (and even a cessation of) bottom trawling, as this activity is prohibited in many OWFs. The long-term cumulative impacts of these changes on marine biodiversity remain largely unknown. This study integrates such impacts into characterization factors for life cycle assessment based on the North Sea and illustrates its application. Our results suggest that there are no net adverse impacts during OWF operation on benthic communities inhabiting the original sand bottom within OWFs. Artificial reefs could lead to a doubling of species richness and a two-order-of-magnitude increase of species abundance. Seabed occupation will also incur in minor biodiversity losses in the soft sediment. Our results were not conclusive concerning the trawling avoidance benefits. The developed characterization factors quantifying biodiversity-related impacts from OWF operation provide a stepping stone toward a better representation of biodiversity in life cycle assessment.

A general framework for species-abundance distributions: Linking traits and dispersal to explain commonness and rarity.

Species-abundance distributions (SADs) describe the spectrum of commonness and rarity in a community. Beyond the universal observation that most species are rare and only a few common, more-precise description of SAD shape is controversial. Furthermore, the mechanisms behind SADs and how they vary along environmental gradients remain unresolved. We lack a general, non-neutral theory of SADs. Here, we develop a trait-based framework, focusing on a local community coupled to the region by dispersal. The balance of immigration and exclusion determines abundances, which vary over orders-of-magnitude. The local trait-abundance distribution (TAD) reflects a transformation of the regional TAD. The left-tail of the SAD depends on scaling exponents of the exclusion function and the regional species pool. More-complex local dynamics can lead to multimodal TADs and SADs. Connecting SADs with trait-based ecological theory provides a way to generate more-testable hypotheses on the controls over commonness and rarity in communities.

Dietary abundance distributions: Dominance and diversity in vertebrate diets.

Diet composition is among the most important yet least understood dimensions of animal ecology. Inspired by the study of species abundance distributions (SADs), we tested for generalities in the structure of vertebrate diets by characterising them as dietary abundance distributions (DADs). We compiled data on 1167 population-level diets, representing >500 species from six vertebrate classes, spanning all continents and oceans. DADs near-universally (92.5%) followed a hollow-curve shape, with scant support for other plausible rank-abundance-distribution shapes. This strong generality is inherently related to, yet incompletely explained by, the SADs of available food taxa. By quantifying dietary generalisation as the half-saturation point of the cumulative distribution of dietary abundance (sp50, minimum number of foods required to account for 50% of diet), we found that vertebrate populations are surprisingly specialised: in most populations, fewer than three foods accounted for at least half the diet. Variation in sp50 was strongly associated with consumer type, with carnivores being more specialised than herbivores or omnivores. Other methodological (sampling method and effort, taxonomic resolution), biological (body mass, frugivory) and biogeographic (latitude) factors influenced sp50 to varying degrees. Future challenges include identifying the mechanisms underpinning the hollow-curve DAD, its generality beyond vertebrates, and the biological determinants of dietary generalisation.

The global impact of management on soil nematode abundances.

Research Highlight: Li, X., Liu, T., Li, H., Geisen, S., Hu, F., & Liu, M. (2022). Management effects on soil nematode abundance differ among functional groups and land-use types at a global scale. Journal of Animal Ecology, https://doi.org/10.1111/1365-2656.13744. Despite the well-documented decline of aboveground species abundances as a result of land-use intensification, there has been little attention on the effects of human activities on belowground species abundances. Li et al. analyse nematode data, the most abundant animal on the planet, from across the globe to determine whether their abundances vary between managed and unmanaged habitats. The authors show that, unlike aboveground biodiversity, nematode abundance is higher in managed than unmanaged primary and secondary habitats. Furthermore, responses to land management vary between trophic groups and they do not appear to follow the general hypothesis that higher trophic levels are more vulnerable to human activity than those further down the food chain, except in urban habitats. Finally, Li et al. show that the relationships between environmental predictors and species abundance were weakened (and sometimes reversed) in managed habitats. Together, their results reveal how land-use management is impacting the trophic composition of soil nematode communities and their relationships with the environment, which has implications for ecosystem functioning.

Species co-occurrence and management intensity modulate habitat preferences of forest birds.

BACKGROUND: Species co-occurrences can have profound effects on the habitat use of species, and therefore habitat structure alone cannot fully explain observed abundances. To account for this aspect of community organization, we developed multi-species abundance models, incorporating the local effect of co-occurring and potentially associated species, alongside with environmental predictors, linked mainly to forest management intensity. We coupled it with a landscape-scale analysis to further examine the role of management intensity in modifying the habitat preferences in connection with the landscape context. Using empirical data from the Black Forest in southern Germany, we focused on the forest bird assemblage and in particular on the cavity-nesting and canopy-foraging guilds. We included in the analysis species that co-occur and for which evidence suggests association is likely. RESULTS: Our findings show that the local effect of species associations can mitigate the effects of management intensity on forest birds. We also found that bird species express wider habitat preferences in forests under higher management intensity, depending on the landscape context. CONCLUSIONS: We suspect that species associations may facilitate the utilization of a broader range of environmental conditions under intensive forest management, which benefits some species over others. Networks of associations may be a relevant factor in the effectiveness of conservation-oriented forest management.

Empirical abundance distributions are more uneven than expected given their statistical baseline.

Exploring and accounting for the emergent properties of ecosystems as complex systems is a promising horizon in the search for general processes to explain common ecological patterns. For example the ubiquitous hollow-curve form of the species abundance distribution is frequently assumed to reflect ecological processes structuring communities, but can also emerge as a statistical phenomenon from the mathematical definition of an abundance distribution. Although the hollow curve may be a statistical artefact, ecological processes may induce subtle deviations between empirical species abundance distributions and their statistically most probable forms. These deviations may reflect biological processes operating on top of mathematical constraints and provide new avenues for advancing ecological theory. Examining ~22,000 communities, we found that empirical SADs are highly uneven and dominated by rare species compared to their statistical baselines. Efforts to detect deviations may be less informative in small communities-those with few species or individuals-because these communities have poorly resolved statistical baselines. The uneven nature of many empirical SADs demonstrates a path forward for leveraging complexity to understand ecological processes governing the distribution of abundance, while the issues posed by small communities illustrate the limitations of using this approach to study ecological patterns in small samples.

An Evolutionary and Ecological Community Model for Distribution of Phenotypes and Abundances among Competing Species.

AbstractHere, we propose a theory for the structure of communities of competing species. We include ecologically realistic assumptions, such as density dependence and stochastic fluctuations in the environment, and analyze how evolution caused by r- and K-selection will affect the packing of species in the phenotypic space as well as the species abundance distribution. Species-specific traits have the same matrix G of additive genetic variances and covariances, and evolution of mean traits is affected by fluctuations in population size of all species. In general, the model produces a shape of the distributions of log abundances that is skewed to the left, which is typical of most natural communities. Mean phenotypes of the species in the community are distributed approximately uniformly on the surface of a multidimensional sphere. However, environmental stochasticity generates selection that deviates species slightly from this surface; nonetheless, phenotypic distribution will be different from a random packing of species. This model of community evolution provides a theoretical framework that predicts a relationship between the structure of the phenotypic space and the form of species abundance distributions that can be compared against time series of variation in community structure.

Defining codominance in plant communities.

Species dominance and biodiversity in plant communities have received considerable attention and characterisation. However, species codominance, while often alleged, is seldom defined or quantified. Codominance is a common phenomenon and is likely to be an important driver of community structure, ecosystem function and the stability of both. Here we review the use of the term 'codominance' and find inconsistencies in its use, suggesting that the scientific community currently lacks a universal understanding of codominance. We address this issue by: (1) qualitatively defining codominance as mostly shared abundance that is distinctively isolated within a subset of a community, and (2) presenting a novel metric for quantifying the degree to which relative abundances are shared among a codominant subset of plant species, while also accounting for the remaining species within a plant community. Using both simulated and real-world data, we then demonstrate the process of applying the codominance metric to compare communities and to generate a quantitatively defensible subset of species to consider codominant within a community. We show that our metric effectively distinguishes the degree of codominance between four types of grassland ecosystems as well as simulated ecosystems with varying degrees of abundance sharing among community members. Overall, we make the case that increased research focusses on the conditions under which codominance occurs and the consequences for species coexistence, community structure and ecosystem function that would considerably advance the fields of community and ecosystem ecology.

Changes in plant species abundance alter the multifunctionality and functional space of heathland ecosystems.

Though it is well established that species composition affects ecosystem function, the way in which species combine to control overall ecosystem functioning is still debated. In experimental mesocosms, we planted three functionally distinct dry-heath species in varying proportions and measured multiple ecosystem properties related to nutrient cycling and carbon storage (hereafter functions). Overall ecosystem functioning was described as the main axes of variation in ecosystem functioning (functional space) and the proportion of ecosystem functions at high levels; for example, fast carbon and nutrient cycling (cluster-based multifunctionality). The first functional space axis, related to nitrogen availability, was driven by plant species abundance, particularly that of legumes, which strongly affected many individual functions. The second, related to total plant biomass and woodiness, was mostly driven by the abundance of dwarf shrubs. Similarly, cluster-based multifunctionality was related to the initial abundance of all species, but particularly the legume. Interactions between species also affected ecosystem multifunctionality, but these effects were smaller in magnitude. These results indicate that species interactions could play a secondary role to species abundance and identity in driving the overall ecosystem functioning of heathlands, but also that axes of variation in functional space are clearly linked to plant functional composition.

Forecast increase in invasive rabbit spread into ecosystems of an oceanic island (Tenerife) under climate change.

The European rabbit (Oryctolagus cuniculus) is a pest and a conservation problem on many islands, where its heavy grazing pressure threatens many endemic plants with extinction. Previous studies in its native and introduced range have highlighted the high spatial variability of rabbit abundance at local and landscape scales, depending on many factors such as the existence of different habitats. Modeling of the species can be useful to better understand spatial patterns and to prioritize actions, especially in those regions in which rabbits have become invasive. Here, we investigate the distribution of the European rabbit in Tenerife (Canary Islands, Spain), where the species was introduced during the 15th century and has subsequently changed vegetation composition. Added to the direct effects of rabbits on vegetation, climate change could also have implications for rabbit populations, especially in the alpine ecosystem. To evaluate that, we estimated rabbit abundance in 216 plots randomly distributed on Tenerife island (61 in the alpine ecosystem), modeled the potential current spatial abundance of the species and considered how it might vary under different climate change scenarios. We associated rabbit abundance to a wide selection of abiotic, biotic, and human variables expected to influence rabbit abundance on the island. We found a positive correlation between rabbit abundance and temperature and a negative correlation in the case of precipitation. Hence, according to the models' projections, climate change is expected to enhance rabbit populations in the future. Current higher densities were related to land disturbance and open areas, and a remarkable increase is expected to occur in the alpine ecosystem. Overall, we consider that this study provides valuable information for land managers in the Canary archipelago as it reveals how global warming could indirectly exacerbate the conservation problems of the endemic flora in oceanic islands.

Effects of soil salinity characteristics on three habitats in inland salt marshes.

Understanding the effect of soil salinity on the diversity and species distribution of plant communities in inland salt marsh ecosystems could provide solutions for the management of regional saline soils and the protection of salt marsh wetland vegetation. A field experiment in succulent halophyte, Carex, and gramineous grass habitats in Ordos, Inner Mongolia (northwest China) was conducted to study the diversity and composition of plants in different saline habitats in inland salt marsh ecosystems. Results showed that plant diversity and species richness in the Carex habitat were significantly higher than the succulent halophyte habitat and the gramineous grass habitat (P < 0.05). Further, species abundance was higher in the succulent halophyte habitat and the Carex habitat than the gramineous grass habitat. Similar results were obtained when considering the abundance of constructive species. No significant differences in the abundance of dominant species and companion species between the gramineous grass habitat and the Carex habitat were found. We concluded that species abundance, species richness, species distribution, and plant diversity together explained the response of plant communities in different habitats to soil salinity, especially Na+ and SO42-. This highlights the importance of soil salinity for the maintenance of plant diversity and structural composition in inland salt marsh ecosystems.

Species functional traits and abundance as drivers of multiplex ecological networks: first empirical quantification of inter-layer edge weights.

Many vertebrate species act as both plant pollinators and seed-dispersers, thus interconnecting these processes, particularly on islands. Ecological multilayer networks are a powerful tool to explore interdependencies between processes; however, quantifying the links between species engaging in different types of interactions (i.e. inter-layer edges) remains a great challenge. Here, we empirically measured inter-layer edge weights by quantifying the role of individually marked birds as both pollinators and seed-dispersers of Galápagos plant species over an entire year. Although most species (80%) engaged in both functions, we show that only a small proportion of individuals actually linked the two processes, highlighting the need to further consider intra-specific variability in individuals' functional roles. Furthermore, we found a high variation among species in linking both processes, i.e. some species contribute more than others to the modular organization of the multilayer network. Small and abundant species are particularly important for the cohesion of pollinator seed-dispersal networks, demonstrating the interplay between species traits and neutral processes structuring natural communities.