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Deterministic theories in community ecology suggest that local, niche-based processes, such as environmental filtering, biotic interactions and interspecific trade-offs largely determine patterns of species diversity and composition. In contrast, more stochastic theories emphasize the importance of chance colonization, random extinction and ecological drift. The schisms between deterministic and stochastic perspectives, which date back to the earliest days of ecology, continue to fuel contemporary debates (e.g. niches versus neutrality). As illustrated by the pioneering studies of Robert H. MacArthur and co-workers, resolution to these debates requires consideration of how the importance of local processes changes across scales. Here, we develop a framework for disentangling the relative importance of deterministic and stochastic processes in generating site-to-site variation in species composition (β-diversity) along ecological gradients (disturbance, productivity and biotic interactions) and among biogeographic regions that differ in the size of the regional species pool. We illustrate how to discern the importance of deterministic processes using nullmodel approaches that explicitly account for local and regional factors that inherently create stochastic turnover. By embracing processes across scales, we can build a more synthetic framework for understanding how niches structure patterns of biodiversity in the face of stochastic processes that emerge from local and biogeographic factors.

Spatial turnover in the composition of biological communities is governed by (ecological) Drift, Selection and Dispersal. Commonly applied statistical tools cannot quantitatively estimate these processes, nor identify abiotic features that impose these processes. For interrogation of subsurface microbial communities distributed across two geologically distinct formations of the unconfined aquifer underlying the Hanford Site in southeastern Washington State, we developed an analytical framework that advances ecological understanding in two primary ways. First, we quantitatively estimate influences of Drift, Selection and Dispersal. Second, ecological patterns are used to characterize measured and unmeasured abiotic variables that impose Selection or that result in low levels of Dispersal. We find that (i) Drift alone consistently governs ∼25% of spatial turnover in community composition; (ii) in deeper, finer-grained sediments, Selection is strong (governing ∼60% of turnover), being imposed by an unmeasured but spatially structured environmental variable; (iii) in shallower, coarser-grained sediments, Selection is weaker (governing ∼30% of turnover), being imposed by vertically and horizontally structured hydrological factors;(iv) low levels of Dispersal can govern nearly 30% of turnover and be caused primarily by spatial isolation resulting from limited exchange between finer and coarser-grain sediments; and (v) highly permeable sediments are associated with high levels of Dispersal that homogenize community composition and govern over 20% of turnover. We further show that our framework provides inferences that cannot be achieved using preexisting approaches, and suggest that their broad application will facilitate a unified understanding of microbial communities.

The abundance and distribution of species across the landscape depend on the interaction between local, spatial, and stochastic processes. However, empirical syntheses relating these processes to spatiotemporal patterns of structure in metacommunities remain elusive. One important reason for this lack of synthesis is that the relative importance of the core assembly processes (dispersal, selection, and drift) critically depends on the spatial grain and extent over which communities are studied. To illustrate this, we simulated different aspects of community assembly on heterogeneous landscapes, including the strength of response to environmental heterogeneity (inherent to niche theory) vs. dispersal and stochastic drift (inherent to neutral theory). We show that increasing spatial extent leads to increasing importance of niche selection, whereas increasing spatial grain leads to decreasing importance of niche selection. The strength of these scaling effects depended on environment configuration, dispersal capacity, and niche breadth. By mapping the variation observed from the scaling effects in simulations, we could recreate the entire range of variation observed within and among empirical studies. This means that variation in the relative importance of assembly processes among empirical studies is largely scale dependent and cannot be directly compared. The scaling coefficient of the relative contribution of assembly processes, however, can be interpreted as a scale-integrative estimate to compare assembly processes across different regions and ecosystems. This emphasizes the necessity to consider spatial scaling as an explicit component of studies intended to infer the importance of community assembly processes.

Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting in biogeochemical hotspots and moments. Riverine systems, where groundwater mixes with surface water (the hyporheic zone), are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. Here, to investigate the coupling among groundwater–surface water mixing, microbial communities and biogeochemistry, we apply ecological theory, aqueous biogeochemistry, DNA sequencing and ultra-high-resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Our results indicate that groundwater–surface water mixing in the hyporheic zone stimulates heterotrophic respiration, alters organic carbon composition, causes ecological processes to shift from stochastic to deterministic and is associated with elevated abundances of microbial taxa that may degrade a broad suite of organic compounds. Groundwater-surface water mixing zones link critical ecosystem domains, but attendant microbe-biogeochemistry-hydrology interactions are poorly known. Here, the authors show that groundwater-surface water mixing stimulates respiration, alters carbon composition, and shifts the ecology from stochastic to deterministic.

Explaining the maintenance of tropical forest diversity under the countervailing forces of drift and competition poses a major challenge to ecological theory. Janzen–Connell effects, in which host-specific natural enemies restrict the recruitment of juveniles near conspecific adults, provide a potential mechanism. Janzen–Connell is strongly supported empirically, but existing theory does not address the stable coexistence of hundreds of species. Here we use high-performance computing and analytical models to demonstrate that tropical forest diversity can be maintained nearly indefinitely in a prolonged state of transient dynamics due to distance-responsive natural enemies. Further, we show that Janzen–Connell effects lead to community regulation of diversity by imposing a diversity-dependent cost to commonness and benefit to rarity. The resulting species–area and rank–abundance relationships are consistent with empirical results. Diversity maintenance over long time spans does not require dispersal from an external metacommunity, speciation, or resource niche partitioning, only a small zone around conspecific adults in which saplings fail to recruit. We conclude that the Janzen–Connell mechanism can explain the maintenance of tropical tree diversity while not precluding the operation of other niche-based mechanisms such as resource partitioning.

Background and aimsSeeds are involved in the transmission of microorganisms from one plant generation to another and consequently may act as the initial inoculum source for the plant microbiota. In this work, we assessed the structure and composition of the seed microbiota of radish (Raphanus sativus) across three successive plant generations.MethodsStructure of seed microbial communities were estimated on individual plants through amplification and sequencing of genes that are markers of taxonomic diversity for bacteria (gyrB) and fungi (ITS1). The relative contribution of dispersal and ecological drift in inter-individual fluctuations were estimated with a neutral community model.ResultsSeed microbial communities of radish display a low heritability across plant generations. Fluctuations in microbial community profiles were related to changes in community membership and composition across plant generations, but also to variation between individual plants. Ecological drift was an important driver of the structure of seed bacterial communities, while dispersal was involved in the assembly of the fungal fraction of the seed microbiota.ConclusionsThese results provide a first glimpse of the governing processes driving the assembly of the seed microbiota.

Historically, the biodiversity and composition of species in a locality was thought to be influenced primarily by deterministic factors. In such cases, species' niches create differential responses to environmental conditions and interspecific interactions, which combine to determine that locality's biodiversity and species composition. More recently, proponents of the neutral theory have placed a premium on how stochastic factors, such as birth, death, colonization, and extinction (termed \"ecological drift\") influence diversity and species composition in a locality independent of their niches. Here, I develop the hypothesis that the relative importance of stochastic ecological drift and/or priority effects depend on the harshness of the ecological filter in those habitats. I established long-term experimental ponds to explore the relative importance of community assembly history and drought on patterns of community compositional similarity among ponds that were otherwise similar in their environmental conditions. I show considerable site-to-site variation in pond community composition in the absence of drought that likely resulted from a combination of stochastic ecological drift and priority effects. However, in ponds that experienced drought, I found much higher similarity among communities that likely resulted from niche-selection filtering out species from the regional pool that could not tolerate such environmental harshness. These results implicate the critical role for understanding the processes of community assembly when examining patterns of biodiversity at different spatial scales.

Aims: Both ecological drift and environmental heterogeneity can produce high beta diversity among communities, but only the effect of drift is expected to be enhanced in communities of small size. Few studies have explicitly tested the influence of community size on patterns of beta diversity. Here we applied a series of analyses aimed at testing the influence of drift versus environmental heterogeneity on beta diversity among tree communities on islands of variable size. Location: Thousand Island Lake, Zhejiang Province, China. Methods: We used data on mapped tree communities and environmental conditions for 20 small islands (<1 ha) and nine large islands (>1 ha) created via the construction of a hydroelectric dam in 1959. Beta diversity was calculated using abundance-based multiple-site dissimilarity based on the Bray–Curtis index. On the basis of the hypothesis of ecological drift among small islands, we tested for higher beta diversity among small than large islands using: (a) raw data (b) controlling for the number of individual sampled on a given island, and (c) controlling for the contiguous sampling area and thus for intra-island environmental heterogeneity. We also tested the prediction that the relationship between species composition and environmental variables should be weaker on small islands using canonical correspondence analyses. Results: Using raw data and controlling for the number of individuals, community dissimilarity was significantly greater among small islands than among large islands. However, when controlling for contiguous sampling area this difference disappeared. Contrary to the prediction based on ecological drift, the strength of overall composition–environment relationships was not significantly weaker for small islands in any of the analyses, and environmental heterogeneity increased faster with area among small islands than among large islands. Main Conclusions: Despite a result using raw data that was consistent with the hypothesis of ecological drift, our full set of results clearly indicated the high beta diversity among small islands was more likely due to environmental heterogeneity rather than ecological drift. This result points to a clear need to control for sampling area among habitats of different size when testing for statistical signatures of drift.

The factors driving β-diversity (variation in community composition) yield insights into the maintenance of biodiversity on the planet. Here we tested whether the mechanisms that underlie bacterial β-diversity vary over centimeters to continental spatial scales by comparing the composition of ammonia-oxidizing bacteria communities in salt marsh sediments. As observed in studies of macroorganisms, the drivers of salt marsh bacterial β-diversity depend on spatial scale. In contrast to macroorganism studies, however, we found no evidence of evolutionary diversification of ammonia-oxidizing bacteria taxa at the continental scale, despite an overall relationship between geographic distance and community similarity. Our data are consistent with the idea that dispersal limitation at local scales can contribute to β-diversity, even though the 16S rRNA genes of the relatively common taxa are globally distributed. These results highlight the importance of considering multiple spatial scales for understanding microbial biogeography.

The coexistence of ecologically similar species might be counteracted by ecological drift and demographic stochasticity, both of which erode local diversity. With niche differentiation, species can be maintained through performance trade-offs between environments, but trade-offs are difficult to invoke for species with similar ecological niches. Such similar species might then go locally extinct due to stochastic ecological drift, but there is little empirical evidence for such processes. Previous studies have relied on biogeographical surveys and inferred process from pattern, while experimental field investigations of ecological drift are rare. Mechanisms preserving local species diversity, such as frequency dependence (e.g., rare-species advantages), can oppose local ecological drift, but the combined effects of ecological drift and such counteracting forces have seldom been investigated. Here, we investigate mechanisms between coexistence of ecologically similar but strongly sexually differentiated damselfly species (Calopteryx virgo and Calopteryx splendens). Combining field surveys, behavioral observations, experimental manipulations of species frequencies and densities, and simulation modeling, we demonstrate that species coexistence is shaped by the opposing forces of ecological drift and negative frequency dependence (rare-species advantage), generated by interference competition. Stochastic and deterministic processes therefore jointly shape coexistence. The role of negative frequency dependence in delaying the loss of ecologically similar species, such as those formed by sexual selection, should therefore be considered in community assembly, macroecology, macroevolution, and biogeography.