Biotic interactions limit species richness in an alpine plant community,especially under experimental warming

The determinants of local species richness in plant communities have been the subject of much debate. Is species richness the result of stochastic events such as dispersal processes, or do local environmental filters sort species into communities according to their ecological niches? Recent studies suggest that these two processes simultaneously limit species richness, although their relative importance may vary in space and time. Understanding the limiting factors for species richness is especially important in light of the ongoing global warming, as new species establish in resident plant communities as a result of climate‐driven migration. We examined the relative importance of dispersal and environmental filtering during seedling recruitment and plant establishment in an alpine plant community subjected to seed addition and long‐term experimental warming. Seed addition increased species richness during the seedling recruitment stage, but this initial increase was cancelled out by a corresponding decrease in species richness during plant establishment, suggesting that environmental filters limit local species richness in the long term. While initial recruitment success of the sown species was related to both abiotic and biotic factors, long‐term establishment was controlled mainly by biotic factors, indicating an increase in the relative importance of biotic interactions once plants have germinated in a microhabitat with favourable abiotic conditions. The relative importance of biotic interactions also seemed to increase with experimental warming, suggesting that increased competition within the resident vegetation may decrease community invasibility as the climate warms.     

Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land,Antarctica

Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment.     

Patterns of environmental variability influence coral‐associated bacterial and algal communities on the Mesoamerican Barrier Reef

A coral's capacity to alter its microbial symbionts may enhance its fitness in the face of climate change. Recent work predicts exposure to high environmental variability may increase coral resilience and adaptability to future climate conditions. However, how this heightened environmental variability impacts coral‐associated microbial communities remains largely unexplored. Here, we examined the bacterial and algal symbionts associated with two coral species of the genus Siderastrea with distinct life history strategies from three reef sites on the Belize Mesoamerican Barrier Reef System with low or high environmental variability. Our results reveal bacterial community structure, as well as alpha‐ and beta‐diversity patterns, vary by host species. Differences in bacterial communities between host species were partially explained by high abundance of Deltaproteobacteria and Rhodospirillales and high bacterial diversity in Siderastrea radians. Our findings also suggest Siderastrea spp. have dynamic core bacterial communities that likely drive differences observed in the entire bacterial community, which may play a critical role in rapid acclimatization to environmental change. Unlike the bacterial community, Symbiodiniaceae composition was only distinct between host species at high thermal variability sites, suggesting that different factors shape bacterial versus algal communities within the coral holobiont. Our findings shed light on how domain‐specific shifts in dynamic microbiomes may allow for unique methods of enhanced host fitness.     

The impact of interactions on invasion and colonization resistance in microbial communities

In human microbiota, the prevention or promotion of invasions can be crucial to human health. Invasion outcomes, in turn, are impacted by the composition of resident communities and interactions of resident members with the invader. Here we study how interactions influence invasion outcomes in microbial communities, when interactions are primarily mediated by chemicals that are released into or consumed from the environment. We use a previously developed dynamic model which explicitly includes species abundances and the concentrations of chemicals that mediate species interaction. Using this model, we assessed how species interactions impact invasion by simulating a new species being introduced into an existing resident community. We classified invasion outcomes as resistance, augmentation, displacement, or disruption depending on whether the richness of the resident community was maintained or decreased and whether the invader was maintained in the community or went extinct. We found that as the number of invaders introduced into the resident community increased, disruption rather than augmentation became more prevalent. With more facilitation of the invader by the resident community, resistance outcomes were replaced by displacement and augmentation. By contrast, with more facilitation among residents, displacement outcomes shifted to resistance. When facilitation of the resident community by the invader was eliminated, the majority of augmentation outcomes turned into displacement, while when inhibition of residents by invaders was eliminated, invasion outcomes were largely unaffected. Our results suggest that a better understanding of interactions within resident communities and between residents and invaders is crucial to predicting the success of invasions into microbial communities.     

Host–microbe interactions as a driver of acclimation to salinity gradients in brown algal cultures

Like most eukaryotes, brown algae live in association with bacterial communities that frequently have beneficial effects on their development. Ectocarpus is a genus of small filamentous brown algae, which comprises a strain that has recently colonized freshwater, a rare transition in this lineage. We generated an inventory of bacteria in Ectocarpus cultures and examined the effect they have on acclimation to an environmental change, that is, the transition from seawater to freshwater medium. Our results demonstrate that Ectocarpus depends on bacteria for this transition: cultures that have been deprived of their associated microbiome do not survive a transfer to freshwater, but restoring their microflora also restores the capacity to acclimate to this change. Furthermore, the transition between the two culture media strongly affects the bacterial community composition. Examining a range of other closely related algal strains, we observed that the presence of two bacterial operational taxonomic units correlated significantly with an increase in low salinity tolerance of the algal culture. Despite differences in the community composition, no indications were found for functional differences in the bacterial metagenomes predicted to be associated with algae in the salinities tested, suggesting functional redundancy in the associated bacterial community. Our study provides an example of how microbial communities may impact the acclimation and physiological response of algae to different environments, and thus possibly act as facilitators of speciation. It paves the way for functional examinations of the underlying host–microbe interactions, both in controlled laboratory and natural conditions.     

A conceptual framework for the spatial analysis of functional trait diversity

Functional trait diversity is a popular tool in modern ecology, mainly used to infer assembly processes and ecosystem functioning. Patterns of functional trait diversity are shaped by ecological processes such as environmental filtering, species interactions and dispersal that are inherently spatial, and different processes may operate at different spatial scales. Adding a spatial dimension to the analysis of functional trait diversity may thus increase our ability to infer community assembly processes and to predict change in assembly processes following disturbance or land‐use change. Richness, evenness and divergence of functional traits are commonly used indices of functional trait diversity that are known to respond differently to large‐scale filters related to environmental heterogeneity and dispersal and fine‐scale filters related to species interactions (competition). Recent developments in spatial statistics make it possible to separately quantify large‐scale patterns (variation in local means) and fine‐scale patterns (variation around local means) by decomposing overall spatial autocorrelation quantified by Moran's coefficient into its positive and negative components using Moran eigenvector maps (MEM). We thus propose to identify the spatial signature of multiple ecological processes that are potentially acting at different spatial scales by contrasting positive and negative components of spatial autocorrelation for each of the three indices of functional trait diversity. We illustrate this approach with a case study from riparian plant communities, where we test the effects of disturbance on spatial patterns of functional trait diversity. The fine‐scale pattern of all three indices was increased in the disturbed versus control habitat, suggesting an increase in local scale competition and an overall increase in unexplained variance in the post‐disturbance versus control community. Further research using simulation modeling should focus on establishing the proposed link between community assembly rules and spatial patterns of functional trait diversity to maximize our ability to infer multiple processes from spatial community structure.     

Does environmental heterogeneity drive functional trait variation? A test in montane and alpine meadows

While community‐weighted means of plant traits have been linked to mean environmental conditions at large scales, the drivers of trait variation within communities are not well understood. Local environmental heterogeneity (such as microclimate variability), in addition to mean environmental conditions, may decrease the strength of environmental filtering and explain why communities support different amounts of trait variation. Here, we assess two hypotheses: first, that more heterogeneous local environments and second, that less extreme environments, should support a broader range of plant strategies and thus higher trait variation. We quantified drivers of trait variation across a range of environmental conditions and spatial scales ranging from sub‐meter to tens of kilometers in montane and alpine plant communities. We found that, within communities, both environmental heterogeneity and environmental means are drivers of trait variation. However, the importance of each environmental factor varied depending on the trait. Our results indicate that larger‐scale trait–climate linkages that hold across communities also apply at small spatial scales, suggesting that microclimate variation within communities is a key driver of community functional diversity. Microclimatic variation provides a potential mechanism for helping to maintain diversity in local communities and also suggests that small‐scale environmental heterogeneity should be measured as a better predictor of functional diversity.     

Community assembly: when should history matter?

Community assembly provides a conceptual foundation for understanding the processes that determine which and how many species live in a particular locality. Evidence suggests that community assembly often leads to a single stable equilibrium, such that the conditions of the environment and interspecific interactions determine which species will exist there. In such cases, regions of local communities with similar environmental conditions should have similar community composition. Other evidence suggests that community assembly can lead to multiple stable equilibria. Thus, the resulting community depends on the assembly history, even when all species have access to the community. In these cases, a region of local communities with similar environmental conditions can be very dissimilar in their community composition. Both regional and local factors should determine the patterns by which communities assemble, and the resultant degree of similarity or dissimilarity among localities with similar environments. A single equilibrium in more likely to be realized in systems with small regional species pools, high rates of connectance, low productivity and high disturbance. Multiple stable equilibria are more likely in systems with large regional species pools, low rates of connectance, high productivity and low disturbance. I illustrate preliminary evidence for these predictions from an observational study of small pond communities, and show important effects on community similarity, as well as on local and regional species richness.     

Predicting species establishment using absent species and functional neighborhoods

Species establishment within a community depends on their interactions with the local environment and resident community. Such environmental and biotic filtering is frequently inferred from functional trait and phylogenetic patterns within communities; these patterns may also predict which additional species can establish. However, differentiating between environmental and biotic filtering can be challenging, which may complicate establishment predictions. Creating a habitat‐specific species pool by identifying which absent species within the region can establish in the focal habitat allows us to isolate biotic filtering by modeling dissimilarity between the observed and biotically excluded species able to pass environmental filters. Similarly, modeling the dissimilarity between the habitat‐specific species pool and the environmentally excluded species within the region can isolate local environmental filters. Combined, these models identify potentially successful phenotypes and why certain phenotypes were unsuccessful. Here, we present a framework that uses the functional dissimilarity among these groups in logistic models to predict establishment of additional species. This approach can use multivariate trait distances and phylogenetic information, but is most powerful when using individual traits and their interactions. It also requires an appropriate distance‐based dissimilarity measure, yet the two most commonly used indices, nearest neighbor (one species) and mean pairwise (all species) distances, may inaccurately predict establishment. By iteratively increasing the number of species used to measure dissimilarity, a functional neighborhood can be chosen that maximizes the detection of underlying trait patterns. We tested this framework using two seed addition experiments in calcareous grasslands. Although the functional neighborhood size that best fits the community's trait structure depended on the type of filtering considered, selecting these functional neighborhood sizes allowed our framework to predict up to 50% of the variation in actual establishment from seed. These results indicate that the proposed framework may be a powerful tool for studying and predicting species establishment.     

Facilitation promotes invasions in plant‐associated microbial communities

While several studies have established a positive correlation between community diversity and invasion resistance, it is less clear how species interactions within resident communities shape this process. Here, we experimentally tested how antagonistic and facilitative pairwise interactions within resident model microbial communities predict invasion by the plant–pathogenic bacterium Ralstonia solanacearum. We found that facilitative resident community interactions promoted and antagonistic interactions suppressed invasions both in the lab and in the tomato plant rhizosphere. Crucially, pairwise interactions reliably explained observed invasion outcomes also in multispecies communities, and mechanistically, this was linked to direct inhibition of the invader by antagonistic communities (antibiosis), and to a lesser degree by resource competition between members of the resident community and the invader. Together, our findings suggest that the type and strength of pairwise interactions can reliably predict the outcome of invasions in more complex multispecies communities.     

Diversity and dynamics of rare and of resident bacterial populations in coastal sands

Coastal sands filter and accumulate organic and inorganic materials from the terrestrial and marine environment, and thus provide a high diversity of microbial niches. Sands of temperate climate zones represent a temporally and spatially highly dynamic marine environment characterized by strong physical mixing and seasonal variation. Yet little is known about the temporal fluctuations of resident and rare members of bacterial communities in this environment. By combining community fingerprinting via pyrosequencing of ribosomal genes with the characterization of multiple environmental parameters, we disentangled the effects of seasonality, environmental heterogeneity, sediment depth and biogeochemical gradients on the fluctuations of bacterial communities of marine sands. Surprisingly, only 3–5% of all bacterial types of a given depth zone were present at all times, but 50–80% of them belonged to the most abundant types in the data set. About 60–70% of the bacterial types consisted of tag sequences occurring only once over a period of 1 year. Most members of the rare biosphere did not become abundant at any time or at any sediment depth, but varied significantly with environmental parameters associated with nutritional stress. Despite the large proportion and turnover of rare organisms, the overall community patterns were driven by deterministic relationships associated with seasonal fluctuations in key biogeochemical parameters related to primary productivity. The maintenance of major biogeochemical functions throughout the observation period suggests that the small proportion of resident bacterial types in sands perform the key biogeochemical processes, with minimal effects from the rare fraction of the communities.     

Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes

The severe environmental stresses of the Arctic may have promoted unique soil bacterial communities compared with those found in lower latitude environments. Here, we present a comprehensive analysis of the biogeography of soil bacterial communities in the Arctic using a high resolution bar‐coded pyrosequencing technique. We also compared arctic soils with soils from a wide range of more temperate biomes to characterize variability in soil bacterial communities across the globe. We show that arctic soil bacterial community composition and diversity are structured according to local variation in soil pH rather than geographical proximity to neighboring sites, suggesting that local environmental heterogeneity is far more important than dispersal limitation in determining community‐level differences. Furthermore, bacterial community composition had similar levels of variability, richness and phylogenetic diversity within arctic soils as across soils from a wide range of lower latitudes, strongly suggesting a common diversity structure within soil bacterial communities around the globe. These results contrast with the well‐established latitudinal gradients in animal and plant diversity, suggesting that the controls on bacterial community distributions are fundamentally different from those observed for macro‐organisms and that our biome definitions are not useful for predicting variability in soil bacterial communities across the globe.     

Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities

Environmental degradation may have strong effects on community assembly processes. We examined the assembly of bacterial and fungal communities in anthropogenically altered and near‐pristine streams. Using pyrosequencing of bacterial and fungal DNA from decomposed alder Alnus incana leaves, we specifically examined if environmental degradation deterministically decreases or increases the compositional turnover of bacterial and fungal communities. Our results showed that near‐pristine streams and anthropogenically altered streams supported distinct fungal and bacterial communities. The mechanisms assembling these communities were different in near‐pristine and altered environments. Environmental disturbance homogenized bacterial communities, whereas fungal communities were more dissimilar in disturbed sites than in near‐pristine sites. Compositional variation of both bacteria and fungi was related to water chemistry variables in disturbed sites, further implying the influence of environmental degradation on community assembly. Bacterial and fungal communities in near‐pristine streams were weakly controlled by environmental factors, suggesting that the relative importance of niche‐based versus neutral processes in assembling microbial communities may strongly depend on the spatial scale and local environmental context. Our results thus suggest that environmental degradation may strongly affect the composition and β‐diversity of stream microbial communities colonizing leaf litter, and that the direction of the change can be different between bacteria and fungi. A better understanding of the environmental tolerances of microbes and the mechanisms assembling microbial communities in natural environmental settings is needed to predict how environmental alteration is likely to affect microbial communities.     

Environmental effects on biofilm bacterial communities: a comparison of natural and anthropogenic factors in New Zealand streams

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Bacterial colonization of Hydra hatchlings follows a robust temporal pattern

Animals are colonized by complex bacterial communities. The processes controlling community membership and influencing the establishment of the microbial ecosystem during development are poorly understood. Here we aimed to explore the assembly of bacterial communities in Hydra with the broader goal of elucidating the general rules that determine the temporal progression of bacterial colonization of animal epithelia. We profiled the microbial communities in polyps at various time points after hatching in four replicates. The composition and temporal patterns of the bacterial communities were strikingly similar in all replicates. Distinct features included high diversity of community profiles in the first week, a remarkable but transient adult-like profile 2 weeks after hatching, followed by progressive emergence of a stable adult-like pattern characterized by low species diversity and the preponderance of the Betaproteobacterium Curvibacter. Intriguingly, this process displayed important parallels to the assembly of human fecal communities after birth. In addition, a mathematical modeling approach was used to uncover the organizational principles of this colonization process, suggesting that both, local environmental or host-derived factor(s) modulating the colonization rate, as well as frequency-dependent interactions of individual bacterial community members are important aspects in the emergence of a stable bacterial community at the end of development.     

Fine-scale spatial patterns in bacterial community composition and function within freshwater ponds

The extent to which non-host-associated bacterial communities exhibit small-scale biogeographic patterns in their distribution remains unclear. Our investigation of biogeography in bacterial community composition and function compared samples collected across a smaller spatial scale than most previous studies conducted in freshwater. Using a grid-based sampling design, we abstracted 100+ samples located between 3.5 and 60 m apart within each of three alpine ponds. For every sample, variability in bacterial community composition was monitored using a DNA-fingerprinting methodology (automated ribosomal intergenic spacer analysis) whereas differences in bacterial community function (that is, carbon substrate utilisation patterns) were recorded from Biolog Ecoplates. The exact spatial position and dominant physicochemical conditions (for example, pH and temperature) were simultaneously recorded for each sample location. We assessed spatial differences in bacterial community composition and function within each pond and found that, on average, community composition or function differed significantly when comparing samples located >20 m apart within any pond. Variance partitioning revealed that purely spatial variation accounted for more of the observed variability in both bacterial community composition and function (range: 24–38% and 17–39%) than the combination of purely environmental variation and spatially structured environmental variation (range: 17–32% and 15–20%). Clear spatial patterns in bacterial community composition, but not function were observed within ponds. We therefore suggest that some of the observed variation in bacterial community composition is functionally ‘redundant''. We confirm that distinct bacterial communities are present across unexpectedly small spatial scales suggesting that populations separated by distances of >20 m may be dispersal limited, even within the highly continuous environment of lentic water.     

A standardized assessment of forest mammal communities reveals consistent functional composition and vulnerability across the tropics

The understanding of global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110–200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g. habitat features and anthropogenic activities) and biotic interactions occur. Here, we used standardized camera trapping data and a novel analytical method that accounts for imperfect detection to assess how the functional composition of terrestrial mammal communities for two traits – trophic guild and body mass – varies across 16 protected areas in tropical forests and three continents, in relation to the extent of protected habitat and anthropogenic pressures. We found that despite their taxonomic differences, communities generally have a consistent trophic guild composition, and respond similarly to these factors. Insectivores were found to be sensitive to the size of protected habitat and surrounding human population density. Body mass distribution varied little among communities both in terms of central tendency and spread, and interestingly, community average body mass declined with proximity to human settlements. Results indicate predicted trait convergence among assemblages at the coarse scale reflects consistent functional composition among communities at the local scale, suggesting that broadly similar habitats and selective pressures shaped communities with similar trophic strategies and responses to drivers of change. These similarities provide a foundation for assessing assemblages under anthropogenic threats and sharing conservation measures.     

Traits linked with species invasiveness and community invasibility vary with time,stage and indicator of invasion in a long‐term grassland experiment

Much uncertainty remains about traits linked with successful invasion – the establishment and spread of non‐resident species into existing communities. Using a 20‐year experiment, where 50 non‐resident (but mostly native) grassland plant species were sown into savannah plots, we ask how traits linked with invasion depend on invasion stage (establishment, spread), indicator of invasion success (occupancy, relative abundance), time, environmental conditions, propagule rain, and traits of invaders and invaded communities. Trait data for 164 taxa showed that invader occupancy was primarily associated with traits of invaders, traits of recipient communities, and invader‐community interactions. Invader abundance was more strongly associated with community traits (e.g. proportion legume) and trait differences between invaders and the most similar resident species. Annuals and invaders with high‐specific leaf area were only successful early in stand development, whereas invaders with conservative carbon capture strategies persisted long‐term. Our results indicate that invasion is context‐dependent and long‐term experiments are required to comprehensively understand invasions.     

Sensitivity of plant functional types to climate change: classification tree analysis of a simulation model

Question: The majority of studies investigating the impact of climate change on local plant communities ignores changes in regional processes, such as immigration from the regional seed pool. Here we explore: (i) the potential impact of climate change on composition of the regional seed pool, (ii) the influence of changes in climate and in the regional seed pool on local community structure, and (iii) the combinations of life history traits, i.e. plant functional types (PFTs), that are most affected by environmental changes. Location: Fire‐prone, Mediterranean‐type shrublands in southwestern Australia. Methods: Spatially explicit simulation experiments were conducted at the population level under different rainfall and fire regime scenarios to determine the effect of environmental change on the regional seed pool for 38 PFTs. The effects of environmental and seed immigration changes on local community dynamics were then derived from community‐level experiments. Classification tree analyses were used to investigate PFT‐specific vulnerabilities to climate change. Results: The classification tree analyses revealed that responses of PFTs to climate change are determined by specific trait characteristics. PFT‐specific seed production and community patterns responded in a complex manner to climate change. For example, an increase in annual rainfall caused an increase in numbers of dispersed seeds for some PFTs, but decreased PFT diversity in the community. Conversely, a simulated decrease in rainfall reduced the number of dispersed seeds and diversity of PFTs. Conclusions: PFT interactions and regional processes must be considered when assessing how local community structure will be affected by environmental change.