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Assemblage similarity decays with geographic distance—a pattern known as the distance–decay relationship. While this pattern has been investigated for a wide range of organisms, ecosystems and geographical gradients, whether these changes vary more cryptically across different forest strata (from ground to canopy) remains elusive. Here, we investigated the influence of ground vs. arboreal assemblages to the general distance–decay relationship observed in forests. We seek to explain differences in distance–decay relationships between strata in the context of the vertical stratification of assemblage composition, richness and abundance. We surveyed for a climate‐sensitive model organism, amphibians, across vertical rainforest strata in Madagascar. For each tree, we defined assemblages of ground‐dwelling, understory, or canopy species. We calculated horizontal distance–decay in similarity across all trees, and across assemblages of species found in different forest strata (ground, understory and canopy). We demonstrate that within stratum comparisons exhibit a classic distance–decay relationship for canopy and understory communities but no distance–decay relationships for ground communities. We suggest that differences in horizontal turnover between strata may be due to local scale habitat and resource heterogeneity in the canopy, or the influence of arboreal traits on species dispersal and distribution. Synthesis. Biodiversity patterns in horizontal space were not consistent across vertical space, suggesting that canopy fauna may not play by the same set of “rules” as their conspecifics living below them on the ground. Our study provides compelling evidence that the above‐ground amphibian assemblage of tropical rainforests is the primary driver of the classical distance–decay relationship. The above‐ground amphibian assemblage of tropical rainforests may be the primary driver of the classical distance–decay relationship.

AIM: Emerging infectious diseases present a major perturbation with apparent direct effects such as reduced population density, extirpation and/or extinction. Comparatively less is known about the potential indirect effects of disease that likely alter community structure and larger ecosystem function. Since 2006, white‐nose syndrome (WNS) has resulted in the loss of over 6 million hibernating bats in eastern North America. Considerable evidence exists concerning niche partitioning in sympatric bat species in this region, and the unprecedented, rapid decline in multiple species following WNS may provide an opportunity to observe a dramatic restructuring of the bat community. LOCATION: We conducted our study at Fort Drum Army Installation in Jefferson and Lewis counties, New York, USA, where WNS first impacted extant bat species in winter 2007–2008. METHODS: Acoustical monitoring during 2003–2011 allowed us to test the hypothesis that spatial and temporal niche partitioning by bats was relaxed post‐WNS. RESULTS: We detected nine bat species pre‐ and post‐WNS. Activity for most bat species declined post‐WNS. Dramatic post‐WNS declines in activity of little brown bat (Myotis lucifugus, MYLU), formerly the most abundant bat species in the region, were associated with complex, often species‐specific responses by other species that generally favoured increased spatial and temporal overlap with MYLU. MAIN CONCLUSIONS: In addition to the obvious direct effects of disease on bat populations and activity levels, our results provide evidence that disease can have cascading indirect effects on community structure. Recent occurrence of WNS in North America, combined with multiple existing stressors, is resulting in dramatic shifts in temporal and spatial niche partitioning within bat communities. These changes might influence long‐term population viability of some bat species as well as broader scale ecosystem structure and function.

The effect of environmental change in structuring the phytoplankton communities of the coastal waters of the Eastern English Channel was investigated by applying a trait-based approach on two decades (1996-2019) of monitoring on diatoms and Phaeocystis . We show that phytoplankton species richness in an unbalanced nutrient supply context was influenced by wind-driven processes, ecological specialization for dissolved inorganic phosphorous, temporal niche differentiation, and a competition-defense and/or a growth-defense trade-off, a coexistence mechanism where weak competitors (i.e., slower growing) are better protected against predation. Under the influence of both environmental perturbations (e.g., wind-driven processes, freshwater influence, unbalanced nutrient levels) and biotic interactions (e.g., competition, predation, facilitation), phytoplankton species exhibited specific survival strategies such as investment on growth, adaptation and tolerance of species to environmental stresses, silicification and resource specialization. These strategies have led to more speciose communities, higher productivity, functional redundancy and stability in the last decade. Our results revealed that the unbalanced nutrient reduction facilitated Phaeocystis blooms and that anthropogenic climate warming and nitrate reduction may threaten the diatom communities of the eastern English Channel in a near future. Our results provide strong support for biogeographical historical and niche-based processes in structuring the phytoplankton community in this temperate region. The variety of species responses that we characterized in this region may help to better understand future changes in pelagic ecosystems, and can serve as a basis to consider functional approaches for future ecosystem management.

Introduction Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitation. However, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among taxa that belong to recently discovered branches of microbial life. Results Here, we assemble metagenomes from tongue and dental plaque samples from multiple individuals and reconstruct 790 non-redundant genomes, 43 of which resolve to TM7, a member of the Candidate Phyla Radiation, forming six monophyletic clades that distinctly associate with either plaque or tongue. Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 group with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and mobilome of cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of microbes. Additionally, we report that prophages are widespread among oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment. Conclusions Our data illuminate niche partitioning of enigmatic members of the oral cavity, including TM7, SR1, and GN02, and provide genomes for poorly characterized yet prevalent members of this biome, such as uncultivated Flavobacteriaceae.

Ecological niche differences are necessary for stable species coexistence but are often difficult to discern. Models of dietary niche differentiation in large mammalian herbivores invoke the quality, quantity, and spatiotemporal distribution of plant tissues and growth forms but are agnostic toward food plant species identity. Empirical support for these models is variable, suggesting that additional mechanisms of resource partitioning may be important in sustaining large-herbivore diversity in African savannas. We used DNA metabarcoding to conduct a taxonomically explicit analysis of large-herbivore diets across southeastern Africa, analyzing ∼4,000 fecal samples of 30 species from 10 sites in seven countries over 6 y. We detected 893 food plant taxa from 124 families, but just two families—grasses and legumes—accounted for the majority of herbivore diets. Nonetheless, herbivore species almost invariably partitioned food plant taxa; diet composition differed significantly in 97% of pairwise comparisons between sympatric species, and dissimilarity was pronounced even between the strictest grazers (grass eaters), strictest browsers (nongrass eaters), and closest relatives at each site. Niche differentiation was weakest in an ecosystem recovering from catastrophic defaunation, indicating that food plant partitioning is driven by species interactions, and was stronger at low rainfall, as expected if interspecific competition is a predominant driver. Diets differed more between browsers than grazers, which predictably shaped community organization: Grazer-dominated trophic networks had higher nestedness and lower modularity. That dietary differentiation is structured along taxonomic lines complements prior work on how herbivores partition plant parts and patches and suggests that common mechanisms govern herbivore coexistence and community assembly in savannas.

Locally, plant species richness supports many ecosystem functions. Yet, the mechanisms driving these often-positive biodiversity–ecosystem functioning relationships are not well understood. Spatial resource partitioning across vertical resource gradients is one of the main hypothesized causes for enhanced ecosystem functioning in more biodiverse grasslands. Spatial resource partitioning occurs if species differ in where they acquire resources and can happen both above- and belowground. However, studies investigating spatial resource partitioning in grasslands provide inconsistent evidence. We present the results of a meta-analysis of 21 data sets from experimental species-richness gradients in grasslands. We test the hypothesis that increasing spatial resource partitioning along vertical resource gradients enhances ecosystem functioning in diverse grassland plant communities above- and belowground. To test this hypothesis, we asked three questions. (1) Does species richness enhance biomass production or community resource uptake across sites? (2) Is there evidence of spatial resource partitioning as indicated by resource tracer uptake and biomass allocation above- and belowground? (3) Is evidence of spatial resource partitioning correlated with increased biomass production or community resource uptake? Although plant species richness enhanced community nitrogen and potassium uptake and biomass production above- and belowground, we found that plant communities did not meet our criteria for spatial resource partitioning, though they did invest in significantly more aboveground biomass in higher canopy layers in mixture relative to monoculture. Furthermore, the extent of spatial resource partitioning across studies was not positively correlated with either biomass production or community resource uptake. Our results suggest that spatial resource partitioning across vertical resource gradients alone does not offer a general explanation for enhanced ecosystem functioning in more diverse temperate grasslands.

Ecological processes underlying bacterial coexistence in the gut are not well understood. Here, we disentangled the effect of the host and the diet on the coexistence of four closely related Lactobacillus species colonizing the honey bee gut. We serially passaged the four species through gnotobiotic bees and in liquid cultures in the presence of either pollen (bee diet) or simple sugars. Although the four species engaged in negative interactions, they were able to stably coexist, both in vivo and in vitro. However, coexistence was only possible in the presence of pollen, and not in simple sugars, independent of the environment. Using metatranscriptomics and metabolomics, we found that the four species utilize different pollen-derived carbohydrate substrates indicating resource partitioning as the basis of coexistence. Our results show that despite longstanding host association, gut bacterial interactions can be recapitulated in vitro providing insights about bacterial coexistence when combined with in vivo experiments. Microbes colonize nearly every environment on Earth, from the ocean and soil to the inner and outer surfaces of animals, such as the gut or skin. They form communities that are usually made up of a diverse range of bacteria, often containing closely related species – a key factor for a successful community. But closely related bacteria can battle for the same resources, so it is unclear how they manage to live alongside each other without competing against one another. While diet is thought to play a key role in enabling closely related bacterial species to co-exist in the gut of an animal, experimental evidence is lacking, due to the difficulty in replicating these systems in the laboratory. One strategy for investigating microbial communities is using honeybees. A major dietary source for honeybees is pollen, which can also be applied in the laboratory to grow diverse types of bacteria found in the honeybee gut. In addition, scientists can generate bees that lack microbial communities in the gut, allowing them to add specific types of bacteria to study their impact. Brochet et al. used this approach with Western honeybees to assess whether diet enables closely related bacteria to live alongside one another in the gut. First, they colonized bees that lacked gut microbes with four closely related bacteria of the genus Lactobacillus , alone or together, and fed the bees either sugar water or sugar water and pollen. After five days, the gut bacteria were analysed. This revealed that bees fed on sugar water only had one dominant Lactobacillus species present in their gut, while bees fed with additional pollen harboured all four Lactobacillus species. Further analysis of these four bacterial species revealed that each of them activates distinct genes when grown on pollen, allowing the different species to consume specific nutrients from broken down pollen. These findings show that closely related bacteria can coexist in the gut by sharing the different nutrients provided in the diet of the host. Consequently, differences in dietary intake in honeybees and other animals may affect the diversity of gut bacteria, and potentially the health of an animal.

Competition plays a central role in the maintenance of biodiversity. A backbone of classic niche theory is that local coexistence of competitors is favoured by the contraction or divergence of species' niches. However, this effect should depend on the diversity of resources available in the local environment, particularly when resources vary in multiple ecological dimensions. Here, we investigated how available resource breadth (i.e. prey diversity) and competition together shape multidimensional niche variation (between and within individuals) and interspecific niche overlap in 42 populations of congeneric tropical frog species. We modelled realized niches in two key trophic dimensions (prey size and carbon stable isotopes) and sampled available food resources to quantify two-dimensional resource breadth. We found a 14-fold variation in multidimensional population niche width across populations, most of which was accounted for by within-individual diet variation. This striking variation was predicted by an interaction whereby individual niche breadth increased with resource breadth and decreased with the number of congeneric competitors. These ecological gradients also interact to influence the degree of niche overlap between species, which surprisingly decreased with population total niche width, providing novel insights on how similar species can coexist in local communities. Together, our results emphasize that patterns of exploitation of resources in multiple dimensions are driven by both competitive interactions and extrinsic factors such as local resource breadth.

The importance of behavioral evolution during speciation is well established, but we know little about how this is manifest in sensory and neural systems. A handful of studies have linked specific neural changes to divergence in host or mate preferences associated with speciation. However, the degree to which brains are adapted to local environmental conditions, and whether this contributes to reproductive isolation between close relatives that have diverged in ecology, remains unknown. Here, we examine divergence in brain morphology and neural gene expression between closely related, but ecologically distinct, Heliconius butterflies. Despite ongoing gene flow, sympatric species pairs within the melpomene–cydno complex are consistently separated across a gradient of open to closed forest and decreasing light intensity. By generating quantitative neuroanatomical data for 107 butterflies, we show that Heliconius melpomene and Heliconius cydno clades have substantial shifts in brain morphology across their geographic range, with divergent structures clustered in the visual system. These neuroanatomical differences are mirrored by extensive divergence in neural gene expression. Differences in both neural morphology and gene expression are heritable, exceed expected rates of neutral divergence, and result in intermediate traits in first-generation hybrid offspring. Strong evidence of divergent selection implies local adaptation to distinct selective optima in each parental microhabitat, suggesting the intermediate traits of hybrids are poorly matched to either condition. Neural traits may therefore contribute to coincident barriers to gene flow, thereby helping to facilitate speciation.