Community Assembly Theory Research Articles

Co-Occurrence Patterns of Aquatic Macroinvertebrates in Laurentian Great Lakes Coastal Wetlands.

In niche-based community assembly theory, it is presumed that communities in habitats with high natural disturbance regimes are less likely to be structured by competitive mechanisms. Laurentian Great Lakes (hereafter Great Lakes) coastal wetlands can experience drastic diel fluctuations in dissolved oxygen levels, severe wave action, ice scour, and near complete freezing during the winter such that conditions are inhospitable for most organisms. The high natural disturbance levels are thought to cause high interannual turnover for aquatic macroinvertebrate communities and support the hypothesis that these communities are less likely to experience less competitive interactions and negative co-occurrence structure. We hypothesize that non-random co-occurrence patterns will be rare in Great Lake coastal wetlands and non-competitive processes (e.g., through shared or differential microhabitat affinities, pollution tolerances, or biotic homogenization) will be more common than competitively driven negative co-occurrence patterns. Null model analysis was performed on 134 macroinvertebrate communities sampled from across the Great Lakes basin from 2000 to 2013. To disentangle the effects of alternative structuring mechanisms (i.e., shared/differential habitat affinities, shared/differential pollution tolerance, and biological homogenization/competitive exclusion), communities were parsed based on the year sampled, the vegetation type from which community samples were collected, and lastly species' functional feeding group assignment or taxonomic group. As expected, very few communities were non-randomly structured; however, all of those that were non-random exhibited showed more negative co-occurrences than by chance. Upon further investigation, these communities consisted of species that are known to overwinter in wetlands, and therefore, avoid having to recolonize after each spring thaw. With expected changes in habitat conditions due to climate change, we propose that null model analyses can be used as an early warning system for community change.

Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient

Interactions between microbiomes and metabolites play crucial roles in the environment, yet how these interactions drive greenhouse gas emissions during ecosystem changes remains unclear. Here we analysed microbial and metabolite composition across a permafrost thaw gradient in Stordalen Mire, Sweden, using paired genome-resolved metagenomics and high-resolution Fourier transform ion cyclotron resonance mass spectrometry guided by principles from community assembly theory to test whether microorganisms and metabolites show concordant responses to changing drivers. Our analysis revealed divergence between the inferred microbial versus metabolite assembly processes, suggesting distinct responses to the same selective pressures. This contradicts common assumptions in trait-based microbial models and highlights the limitations of measuring microbial community-level data alone. Furthermore, feature-scale analysis revealed connections between microbial taxa, metabolites and observed CO2 and CH4 porewater variations. Our study showcases insights gained by using feature-level data and microorganism–metabolite interactions to better understand metabolic processes that drive greenhouse gas emissions during ecosystem changes.

Predicting the first steps of evolution in randomly assembled communities

Microbial communities can self-assemble into highly diverse states with predictable statistical properties. However, these initial states can be disrupted by rapid evolution of the resident strains. When a new mutation arises, it competes for resources with its parent strain and with the other species in the community. This interplay between ecology and evolution is difficult to capture with existing community assembly theory. Here, we introduce a mathematical framework for predicting the first steps of evolution in large randomly assembled communities that compete for substitutable resources. We show how the fitness effects of new mutations and the probability that they coexist with their parent depends on the size of the community, the saturation of its niches, and the metabolic overlap between its members. We find that successful mutations are often able to coexist with their parent strains, even in saturated communities with low niche availability. At the same time, these invading mutants often cause extinctions of metabolically distant species. Our results suggest that even small amounts of evolution can produce distinct genetic signatures in natural microbial communities.

Predicting the First Steps of Evolution in Randomly Assembled Communities.

Microbial communities can self-assemble into highly diverse states with predictable statistical properties. However, these initial states can be disrupted by rapid evolution of the resident strains. When a new mutation arises, it competes for resources with its parent strain and with the other species in the community. This interplay between ecology and evolution is difficult to capture with existing community assembly theory. Here, we introduce a mathematical framework for predicting the first steps of evolution in large randomly assembled communities that compete for substitutable resources. We show how the fitness effects of new mutations and the probability that they coexist with their parent depends on the size of the community, the saturation of its niches, and the metabolic overlap between its members. We find that successful mutations are often able to coexist with their parent strains, even in saturated communities with low niche availability. At the same time, these invading mutants often cause extinctions of metabolically distant species. Our results suggest that even small amounts of evolution can produce distinct genetic signatures in natural microbial communities.

Mean landscape‐scale incidence of species in discrete habitats is patch size dependent

AbstractAimA pervasive negative relationship between the species richness of an assemblage and the mean global range size of the species it contains has recently been identified. Here, we test for an effect of habitat patch size on the mean landscape‐scale incidence (estimating local range size) of constituent species independent of variation in richness.LocationGlobal.Time PeriodContemporary.Major Taxa StudiedVarious.MethodsWe devised a new standardized patch‐scale metric, Mean Species Landscape‐scale Incidences per Patch (MSLIP). Positive values indicate a patch contains more widespread (high‐incidence) species than expected relative to their frequency in the landscape; negative values indicate the presence of more narrow‐range (low‐incidence) species. For 202 metacommunity datasets (archipelagos, habitat islands and fragments) we regressed MSLIP on patch size, testing four hypotheses: (i) no effect (zero slope), (ii) more widespread species in smaller patches (negative slope), (iii) more narrow‐range species in smaller patches (positive slope), (iv) a composite effect (curvilinear/unimodal).ResultsThere was a generally negative curvilinear relationship between MSLIP and patch size, consistent with smaller and larger patches respectively containing more high‐ and low‐incidence species than expected. At intermediate patch sizes, mean species incidence approximates that of the overall landscape. Relative richness mediated this relationship; species‐rich sites of any size increasingly favoured low‐incidence species, species‐poor sites high‐incidence species. Results were consistent for taxonomic groups, and metacommunity types, except aquatic habitat islands.Main ConclusionsThe dependence of mean species incidence on both patch size and relative richness has implications for biodiversity and community assembly theory, or when seeking to understand ecological processes sensitive to species composition (e.g., ecosystem functioning, trophic web structures). We propose the ‘patch size where the MSLIP regression intersects zero’ as a benchmark distinguishing smaller from larger patches, with the expectation small patches preferentially support more high‐incidence and large patches more low‐incidence species.

Assembly mechanisms of microbial communities in plastisphere related to species taxonomic types and habitat niches

A lot of plastic floats are presented in the kelp cultivation zone, enabling us to effectively evaluate the differences between surface water (SW) and plastic-attached (PA) microbial communities. In this study, we explored the microbial communities (both bacteria and protists) in SW and PA niches during the kelp cultivation activities. Effects of habitat niches on the diversity and composition of microbial communities were found. Beta partitioning and core taxa analyses showed species turnover and local species pool governed the microbial community assembly, and they contributed more to bacteria and protists, respectively. Based on the results of null model, bacterial communities presented a more deterministic and homogeneous assembly compared to protistan communities. Moreover, microbial communities in PA niche had higher species turnover and homogenizing assembly compared to the SW niche. The results of this study supplemented the theory of microbial community assembly and expanded our understanding of protists in plastisphere.

Applying community assembly theory to restoration: overcoming dispersal and abiotic filters is key to diversifying California grassland

Ecologists have explored community assembly through the framework of ecological filters, which predicts that species must overcome a series of challenges (i.e. pass through “filters”) to successfully establish in a given community. In the context of restoration, these filters (dispersal, abiotic, and biotic) can be manipulated to alter the resulting plant community by favoring native species or disadvantaging non‐native invasive species. We conducted two studies manipulating assembly filters at two California grassland sites previously dominated by non‐native species. At Site 1, we explored how variations in sequential seeding of native grasses and forbs (to overcome dispersal and biotic filters caused by priority effects) influenced the resulting community. At Site 2, we explored how thatch removal (to overcome the abiotic filter of light limitation) and herbicide‐based weed control (to overcome the biotic filter of competition from non‐native species) influenced the addition of native forbs into a partially restored grassland. Native forbs at Site 1 did not suffer from arriving after grasses, but native grasses benefited when given 1 year priority over forbs. At Site 2, dethatching increased native forb cover in a high rainfall year. Herbicide application reduced non‐native grass cover in dethatched plots without negatively affecting native cover. Native forb and grass cover were significant predictors of non‐native grass cover. However, they accounted for only 29% of the variation observed, suggesting there are other influential factors not considered in this study. Our results suggest that forbs can be incorporated into established native grasslands more successfully after dethatching.

Chance and necessity in the assembly of plant communities: Stochasticity increases with size, isolation and diversity of temporary ponds

Abstract Biodiversity emerges from niche mechanisms, in which the combination of traits determines species performance, and populations drift because of the inherent stochasticity of community assembly processes. Population biology dictates that small and isolated communities are more prone to show stochastic assemblages. However, a reduced mass effect in isolated communities may promote trait selection. In addition, large and connected communities have a larger species pool, higher functional redundancy, lower population sizes and more random recruitment, which also fosters stochasticity in community assembly. These contradictory expectations demand empirical analyses. Plant metacommunities in temporary ponds are assembled by the action of strong environmental filters and cover wide ranges of local community sizes and connectivity, representing ideal systems for identifying determinants of trait‐selection processes. Using a deviance partition method introduced by the theory of community assembly by trait selection, we evaluated the role of plant traits in local community assemblies along 60 communities from a 14‐year plant survey of temporary ponds. Variation in pond size, hydroperiod, connectitivity and heterogeneity determined a selection gradien in traits related to drought resistance, life history and disperal strategies; and also in the strength of trait‐mediated community assembly. The taxonomic and functional diversity of a pond and its physical heterogeneity fostered stochasticity in the assembly of the community, which also presented a hump‐shaped association with connectivity. The pond area increased taxonomic richness but decreased functional diversity, determining negative and positive indirect effects on stochasticity. Synthesis. Diversity provides the raw material for trait selection putatively reducing stochasticity, but here diversity was positively related to stochasticity. Having enough functional diversity, larger redundancy and lower population sizes in diverse communities is probably fostering stochastic assemblages. The hump‐shaped association between stochasticity and connectivity supports a larger role of trait selection in isolated systems due to a weak mass effect, but also on connected communities in which a set of more optimal traits for the selection scenario could be available. In the ongoing state of ecosystem fragmentation, these empirical trends contribute to the mechanistic understanding of the connection between landscape structure and biodiversity assembly.

Bacterial communities exhibit apparent phosphate concentration-related patterns of community composition, alpha diversity, and phylogenetic structure in the subtropical Daya Bay

Increasing anthropogenic activities have caused serious environmental problems and undesirable ecological impacts on bay ecosystems. However, much remains to be learned regarding marine bacterial community assembly and its underlying mechanisms under intensive anthropogenic activities in subtropical bays. In this study, we used the community assembly theory to analyze bacterial community distributions in the subtropical Daya Bay, where the habitats are subject to serious thermal discharge and excessive nutrient load. We found the community assembly of bacterial in the Daya Bay was dominantly shaped by environmental factor of seawater phosphate, followed by temperature, and silicate. High phosphate concentration significantly increased the relative abundance of Actinobacteria, Cyanobacteria, Planctomycetes, and Gammaprotecteria, but reduced the relative abundance of Bacteroidetes and Alphaproteobacteria. Moreover, higher phosphate concentration was found significantly and positively correlated with higher bacterial alpha diversity. Compared with stochastic processes, we found higher phosphate concentration imposed stronger deterministic processes (primarily homogeneous selection) in structuring bacterial community assembly in the subtropical Daya bay, and bacterial communities tended to be higher phylogenetically clustered in higher phosphate-concentration habitats. In summary, we proposed that phosphate is a major environmental determinant in the subtropical Daya Bay and influenced the relative importance of deterministic and stochastic processes in bacterial community assembly.

Scale-dependent changes in species richness caused by invader competition

Ecologists have produced substantial literature about the impact of biological invasions on species diversity. However, due to scale-dependent factors, no consistent conclusion has been reached regarding whether biological invasion leads to a loss of species diversity. In this project, we incorporate an invasion scenario into community assembly theories through spatially explicit individual-based models. We explore how invader dominance shifts community richness at local scales and how local-scale extinctions translate to broader scales. To do so, native community dynamics are simulated according to the niche-neutral continuum theory and constructed on a heterogeneous landscape with a limited environmental gradient. We synthetically assume that the establishment of invaders is wholly affected by their niche or fitness difference from native populations. By analyzing richness changes across all sample sizes, we obtained the following results: (1) for randomly distributed habitat resources, the magnitude of richness loss linearly decreases with sample size when strong niche overlap occurs, but the magnitude is more nonlinearly shaped in communities assembled by niche departures; (2) spatially structured native populations could have greater resistance to invasion competition, and if on clustered habitats and the species suffering more niche overlap, then larger extinction events would occur at broader scales; and (3) these invasion modification trends could be linked with native population spatial structures and abundance evenness. The above findings are solely based on simulation experiments and implemented under several synthetic assumptions. This suggests theoretical linkages between invasion scale-dependent influences and mechanistic issues, such as the properties of the invader and invaded communities, which can inform invasive species management and restoration.

Heterogeneity of CH4-derived carbon induced by O2:CH4 mediates the bacterial community assembly processes

The mechanism by which O2:CH4 controls microbial community assembly in the process of aerobic methane oxidation coupled to denitrification (AMED) remains largely uncharacterized, which hinders the design of engineering microbiomes for the AMED. In this study, the changes in the bacterial community in fed-batch serum bottle reactors under different O2:CH4 ratios were systematically characterized. The ratios of CH4 consumption to the amount of nitrate removal in the treatment with O2:CH4 = 1.5:1, O2:CH4 = 0.5:1, and O2:CH4 = 0.25:1 were 13.1 ± 3.4, 4.7 ± 1.1, and 5.9 ± 3.0 mol-CH4 mol−1-NO3−, respectively. The α-diversity of the bacterial community increased as O2:CH4 decreased. Significantly different selection patterns were found for the high and low O2:CH4 ratios. The coherence process dominated the selection at high O2:CH4 ratios, while the diversification process played a role when O2:CH4 was low. Differences were also observed in the composition of CH4-derived carbon between treatments with O2:CH4 = 1.5:1 and O2:CH4 = 0.5:1. Compared with the treatments with O2:CH4 = 1.5:1, the concentrations of methanol, formaldehyde, acetate, and ethanol in the treatment with O2:CH4 = 0.5:1 were significantly higher, while the concentration of formate was significantly lower. The heterogeneity of CH4-derived carbon induced by O2:CH4 was likely to be responsible for the differences in the selection patterns. Our findings bridge the gaps between the observations of bacterial community perturbations and ecological community assembly theories, highlighting the potential of the bottom-up design approach to improve the nitrate removal rate of the AME-D.

Environmental Filtering Influences Functional Community Assembly of Epibenthic Communities

Community assembly theory states that species assemble non-randomly as a result of dispersal limitation, biotic interactions, and environmental filtering. Strong environmental filtering likely leads to local assemblages that are similar in their functional trait composition (high trait convergence) while functional trait composition will be less similar (high trait divergence) under weaker environmental filters. We used two Arctic shelves as case studies to examine the relationship between functional community assembly and environmental filtering using the geographically close but functionally and environmentally dissimilar epibenthic communities on the Chukchi and Beaufort Sea shelves. Environmental drivers were compared to functional trait composition and to trait convergence within each shelf. Functional composition in the Chukchi Sea was more strongly correlated with environmental gradients compared to the Beaufort Sea, as shown by a combination of RLQ and fourth corner analyses and community-weighted mean redundancy analyses. In the Chukchi Sea, epibenthic functional composition, particularly body size, reproductive strategy, and several behavioral traits (i.e., feeding habit, living habit, movement), was most strongly related to gradients in percent mud and temperature while body size and larval development were most strongly related to a depth gradient in the Beaufort Sea. The stronger environmental filter in the Chukchi Sea also supported the hypothesized relationship with higher trait convergence, although this relationship was only evident at one end of the observed environmental gradient. Strong environmental filtering generally provides a challenge for biota and can be a barrier for invading species, a growing concern for the Chukchi Sea shelf communities under warming conditions. Weaker environmental filtering, such as on the Beaufort Sea shelf, generally leads to communities that are more structured by biotic interactions, and possibly representing partitioning of resources among species from intermediate disturbance levels. We provide evidence that environmental filtering can structure functional community composition, providing a baseline of how community function could be affected by stressors such as changes in environmental conditions or increased anthropogenic disturbance.

Palm Functional Traits, Soil Fertility and Hydrology Relationships in Western Amazonia

Quantification of multivariate trait spectra (or axes of specialization) make the definition of plant strategies more operational, which promotes trait-based theory of community assembly and the understanding of dynamics and functioning of ecosystems. We used field-quantified soil data to explore trait-environment relationships across palm communities in western Amazonia. We collected data from 116 palm species in 458 transects across four distinct forest types. We combined these data with trait records to relate local plant community trait composition to broad gradients in soil variables and forest types. There were significant trait-environment relationships across western Amazonia. Palms with large leaves and fruits, and palms with both growth forms (acaulescent/erect) were associated with fertile soils, while palms with unarmed leaves and stems were associated with non-inundated environments. These results suggest that the functional traits of palms vary consistently along soil gradients on a regional scale. This variation could be explained by the soil fertility and acidity + aluminum gradients, suggesting environmental filters related to resource availability and stressful environments, such as acid soils and soils with high aluminum content.

Exploration of the Types of Rarity in the Arctic Ocean from the Perspective of Multiple Methodologies.

The Arctic Ocean is facing rapid environmental changes with cascading effects on the entire Arctic marine ecosystem. However, we have a limited understanding of the consequences such changes have on bacteria and archaea (prokaryotes) at the base of the marine food web. In this study, we show how the prokaryotic rare biosphere behaves over a range of highly heterogeneous environmental conditions using 16S rRNA gene reads from amplicon and metagenome sequencing data from seawater samples collected during the Norwegian young sea ICE expedition between late winter and early summer. The prokaryotic rare biosphere was analyzed using different approaches: amplicon sequence variants and operational taxonomic units from the 16S rRNA gene amplicons and operational taxonomic units from the 16S rRNA genes of the metagenomes. We found that prokaryotic rare biosphere communities are specific to certain water masses, and that the majority of the rare taxa identified were always rare and disappeared in at least one sample under changing conditions, suggesting their high sensitivity to environmental heterogeneity. In addition, our methodological comparison revealed a good performance of 16S rRNA gene amplicon sequencing in describing rare biosphere patterns, while the metagenome-derived data were better to capture a significant diversity of so-far uncultivated rare taxa. Our analysis on the dynamics of the rare prokaryotic biosphere, by combining different methodological approaches, improves the description of the types of rarity predicted from Community Assembly theory in the Arctic Ocean.

Incorporating human behaviors into theories of urban community assembly and species coexistence

In cities, humans directly and indirectly affect plant and wildlife communities. These human–species interactions are not included in traditional ecological approaches used to understand why and how organisms are distributed. Here, we incorporate human behaviors into urban community assembly theories and detail all the complex ways humans affect the dispersal, selection and persistence of species in cities. To do this, we integrate human behaviors and actions into traditional filter frameworks used to study community assembly. We use our framework to develop testable hypotheses to predict patterns of urban diversity as well as pose key considerations for future research. In order to have a predictive understanding of how urban biodiversity responds to environmental, social and land use change, it is necessary to better understand interactions between humans and other organisms.

How phenological tracking shapes species and communities in non-stationary environments.

Climate change alters the environments of all species. Predicting species responses requires understanding how species track environmental change, and how such tracking shapes communities. Growing empirical evidence suggests that how species track phenologically - how an organism shifts the timing of major biological events in response to the environment - is linked to species performance and community structure. Such research tantalizingly suggests a potential framework to predict the winners and losers of climate change, and the future communities we can expect. But developing this framework requires far greater efforts to ground empirical studies of phenological tracking in relevant ecological theory. Here we review the concept of phenological tracking in empirical studies and through the lens of coexistence theory to show why a community-level perspective is critical to accurate predictions with climate change. While much current theory for tracking ignores the importance of a multi-species context, basic community assembly theory predicts that competition will drive variation in tracking and trade-offs with other traits. We highlight how existing community assembly theory can help understand tracking in stationary and non-stationary systems. But major advances in predicting the species- and community-level consequences of climate change will require advances in theoretical and empirical studies. We outline a path forward built on greater efforts to integrate priority effects into modern coexistence theory, improved empirical estimates of multivariate environmental change, and clearly defined estimates of phenological tracking and its underlying environmental cues.

Coexistence holes fill a gap in community assembly theory.

Coexistence holes fill a gap in community assembly theory.

Impacts of Land-Use Changes on Vegetation and Ecosystem Functioning: Old-Field Secondary Succession.

The study of ecological succession to determine how plant communities re-assemble after a natural or anthropogenic disturbance has always been an important topic in ecology. The understanding of these processes forms part of the new theories of community assembly and species coexistence, and is attracting attention in a context of expanding human impacts. Specifically, new successional studies provide answers to different mechanisms of community assemblage, and aim to define the importance of deterministic or stochastic processes in the succession dynamic. Biotic limits, which depend directly on biodiversity (i.e., species competition), and abiotic filtering, which depends on the environment, become particularly important when they are exceeded, making the succession process more complicated to reach the previous disturbance stage. Plant functional traits (PFTs) are used in secondary succession studies to establish differences between abandonment stages or to compare types of vegetation or flora, and are more closely related to the functioning of plant communities. Dispersal limitation is a PFT considered an important process from a stochastic point of view because it is related to the establishing of plants. Related to it the soil seed bank plays an important role in secondary succession because it is essential for ecosystem functioning. Soil compounds and microbial community are important variables to take into account when studying any succession stage. Chronosequence is the best way to study the whole process at different time scales. Finally, our objective in this review is to show how past studies and new insights are being incorporated into the basis of classic succession. To further explore this subject we have chosen old-field recovery as an example of how a number of different plant communities, including annual and perennial grasslands and shrublands, play an important role in secondary succession.

Multi-Replicated Enrichment Communities as a Model System in Microbial Ecology.

Recent advances in robotics and affordable genomic sequencing technologies have made it possible to establish and quantitatively track the assembly of enrichment communities in high-throughput. By conducting community assembly experiments in up to thousands of synthetic habitats, where the extrinsic sources of variation among replicates can be controlled, we can now study the reproducibility and predictability of microbial community assembly at different levels of organization, and its relationship with nutrient composition and other ecological drivers. Through a dialog with mathematical models, high-throughput enrichment communities are bringing us closer to the goal of developing a quantitative predictive theory of microbial community assembly. In this short review, we present an overview of recent research on this growing field, highlighting the connection between theory and experiments and suggesting directions for future work.

Ecological drivers of avian community assembly along a tropical elevation gradient

Community assembly theory hypothesizes that two main niche‐based processes act to shape composition and organization of biological assemblages: abiotic filtering and biological interactions. Here, we conducted repeated surveys of bird abundance along an undisturbed elevational gradient in the tropical Andes to investigate 1) signals of deterministic processes driving community assembly and 2) potential mechanisms by which these forces operate (temperature, habitat complexity, fruit and insect availability), while correcting for imperfect detection and modeling species abundances with N‐mixture models. We observed strong signals of abiotic filtering driving functionally and phylogenetically clustered assemblages towards higher elevations, and a weaker signal of limiting similarity resulting in few overdispersed assemblages at lower elevations. Whereas the decay in species richness with increasing elevation was explained by temperature, trait and phylogenetic dispersion were explained by both temperature and vegetation structure, implying that an interplay of abiotic and biotic mechanisms determines abundance‐based community structure in our montane assemblages. Interestingly, trait and phylogenetic dispersion consistently decreased until ~3000 m but increased above this elevation, highlighting a potential role of competition in resource‐scarce habitats. Combined, our findings suggest abiotic filters are still the main process shaping montane biotas across elevations, whereas resource availability might act locally upon assemblages further modifying them. Our study challenges recent studies in tropical mountains that suggest that biotic filters are a stronger force than abiotic filters in shaping tropical montane assemblages, and exemplifies how accounting for imperfect detection might overcome potential biases in detecting environmental filtering signals in community assembly studies.