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Ecological disturbances are often hypothesized to alter community assembly processes that influence variation in community composition (β‐diversity). Disturbance can cause convergence in community composition (low β‐diversity) by increasing niche selection of disturbance‐tolerant species. Alternatively, disturbance can cause divergence in community composition (high β‐diversity) by increasing habitat filtering across environmental gradients. However, because disturbance may also influence β‐diversity through random sampling effects owing to changes in the number of individuals in local communities (community size) or abundances in the regional species pool, observed patterns of β‐diversity alone cannot be used to unambiguously discern the relative importance of community assembly mechanisms. We compared β‐diversity of woody plants and inferred assembly mechanisms among unburned forests and forests managed with prescribed fires in the Missouri Ozarks, USA. Using a null‐model approach, we compared how environmental gradients influenced β‐diversity after controlling for differences in local community size and regional species abundances between unburned and burned landscapes. Observed β‐diversity was higher in burned landscapes. However, this pattern disappeared or reversed after controlling for smaller community size in burned landscapes. β‐diversity was higher than expected by chance in both landscapes, indicating an important role for processes that create clumped species distributions. Moreover, fire appeared to decrease clumping of species at broader spatial scales, suggesting homogenization of community composition through niche selection of disturbance‐tolerant species. Environmental variables, however, explained similar amounts of variation in β‐diversity in both landscapes, suggesting that disturbance did not alter the relative importance of habitat filtering. Our results indicate that contingent responses of communities to fire reflect a combination of fire‐induced changes in local community size and scale‐dependent effects of fire on species clumping across landscapes. Synthesis. Although niche‐based mechanisms of community assembly are often invoked to explain changes in community composition following disturbance, our results suggest that these changes also arise through random sampling effects owing to the influence of disturbance on community size. Comparative studies of these processes across disturbed ecosystems will provide important insights into the ecological conditions that determine when disturbance alters the interplay of deterministic and stochastic processes in natural and human‐modified landscapes.

There is increasing recognition that community assembly theory can offer valuable insights for ecological restoration. We studied community assembly processes following tropical forest restoration efforts, using dung beetles (Scarabaeinae) as a focal taxon to investigate taxonomic and functional patterns of biodiversity recovery. We evaluated the relative importance of the local environment (i.e., canopy cover, understory cover, tree basal area, and soil texture), landscape context (i.e., habitat patch proximity and availability and percentage of surrounding area classified as natural forest or Eucalyptus spp. plantation), and space (i.e., spatial proximity of the study areas to estimate dispersal limitation or unmeasured spatially structured processes) on dung beetle species and functional trait composition across a gradient of 15 restoration sites in Brazilian Atlantic Forest. We also assessed which factors were the primary determinants in the establishment of individual dung beetle functional groups, classified according to size, food relocation habit, diet, and period of flight activity. Both species and functional trait composition were most strongly influenced by the local environment, indicating that assembly was predominantly driven by niche-based processes. Most of the variation explained by space was co-explained by local environment and landscape context, ruling out a strong influence of dispersal limitation and random colonization on assembly following restoration. In addition, nearly all of the variance explained by landscape context was coexplained by local environment, suggesting that arrival and establishment at a site depends on both local and landscape-scale environmental factors. Despite strong evidence for niche-based assembly, a large amount of variation remained unexplained in all models, suggesting that stochastic processes and/or unmeasured environmental variables also play an important role. The relative importance of local environment, landscape context, and space changed considerably when analyzing the assembly mechanisms of each functional group separately. Therefore, to recover distinct functional traits in restoration sites, it may be necessary to manipulate different components of the local environment and surrounding landscape. Overall, this study shows that assembly rules can help to better understand recovery processes, enabling improvement of future restoration efforts.

Natural ecosystems show variable resistance to invasion by alien species, and this resistance can relate to the species diversity in the system. In soil, microorganisms are key components that determine life support functions, but the functional redundancy in the microbiota of most soils has long been thought to overwhelm microbial diversity–function relationships. We here show an inverse relationship between soil microbial diversity and survival of the invading species Escherichia coli O157:H7, assessed by using the marked derivative strain T. The invader's fate in soil was determined in the presence of (i) differentially constructed culturable bacterial communities, and (ii) microbial communities established using a dilution-to-extinction approach. Both approaches revealed a negative correlation between the diversity of the soil microbiota and survival of the invader. The relationship could be explained by a decrease in the competitive ability of the invader in species-rich vs. species-poor bacterial communities, reflected in the amount of resources used and the rate of their consumption. Soil microbial diversity is a key factor that controls the extent to which bacterial invaders can establish.

The roles of species richness, resource use, and resource availability are central to many hypotheses explaining the diversity-invasion phenomenon but are generally not investigated together. Here, we created a large diversity gradient of soil microbial communities by either assembling communities of pure bacterial strains or removing the diversity of a natural soil. Using data on the resource-use capacities of the soil communities and an invader that were gathered from 71 carbon sources, we quantified the niches available to both constituents by using the metrics community niche and remaining niche available to the invader. A strong positive relationship between species richness and community niche across both experiments indicated the presence of resource complementarity. Moreover, community niche and the remaining niche available to the invader predicted invader abundance well. This suggested that increased competition in communities of higher diversity limits community invasibility and underscored the importance of resource availability as a key mechanism through which diversity hinders invasions. As a proof of principle, we subjected selected invaded communities to a resource pulse, which progressively uncoupled the link between soil microbial diversity and invasion and allowed the invader to rebound after nearly being eliminated in some communities. Our results thus show that (1) resource competition suppresses invasion, (2) biodiversity increases resource competition and decreases invasion through niche preemption, and (3) resource pulses that cannot be fully used, even by diverse communities, are favorable to invasion.

If natural communities are assembled according to deterministic rules, coexisting species will represent a nonrandom subset of the potential species pool. We tested for signatures of assembly rules in the distribution of species' traits in Pacific rockfish (Sebastes spp.) assemblages. We used morphology, dietary niche (estimated with stable nitrogen isotopes), and distribution data to identify traits that relate to local-scale resource use (the α-niche) and to environmental gradients (the β-niche). We showed that gill raker morphology was related to trophic position (an α-niche axis), while relative eye size was associated with depth habitat (a β-niche axis). We therefore hypothesized that, within assemblages of coexisting rockfish species, the gill raker trait would be overdispersed (evenly spaced) due to limiting similarity, while relative eye size would be clustered due to environmental filtering. We examined the evolutionary relatedness of coexisting species to ask whether phylogenetic community structure and trait distributions gave similar indications about the roles of assembly processes. We tested the trait distributions and phylogenetic structure of 30 published rockfish assemblages against a null model of random community assembly. As predicted, the gill raker trait tended to be more evenly spaced than expected by chance, as did overall body size, while relative eye size was more clustered than expected. Phylogenetic community structure appeared to reflect historical dispersal and speciation and did not provide consistent support for assembly rules. Our results indicate that rockfish community assembly is nonrandom with regard to species' traits and show how distinguishing traits related to the α- and β-niches and incorporating functional morphology can provide for powerful tests of assembly rules.

Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.

Changing nutrient concentrations and introduction of non-native species affect the energy and nutrient fluxes in aquatic ecosystems. As a response, invertebrate communities could be altered, and ‘novel’ trophic communities could develop. Lake Constance (Europe) experienced pronounced nutrient variation caused by cultural eutrophication (prior 1980s) and oligotrophication (post-1980) and experienced many neobiota invasions. We used archived samples to investigate the impact of oligotrophication and invasive species on carbon and nitrogen isotope signatures of littoral macroinvertebrates during spring and autumn periods from 2000 to 2015 and of littoral fish species in 2018. Isotopic signatures of invertebrate and fish species were in the same range and showed similar seasonal differences and clear patterns in respect to littoral vs pelagic food sources and trophic level. Oligotrophication did not strongly alter isotopic values and only δ15N values of invertebrates declined weakly with oligotrophication. In contrast, interannual variability of stable isotope signatures was related to abundances of the invasive Dreissena polymorpha suggesting interannual differences in the importance of benthic-pelagic coupling due to Dreissena pseudofaeces for the nutrition of littoral invertebrates. This study illustrates how stored samples can be used to detect the importance of oligotrophication and benthic-pelagic coupling on the stable isotope signatures of a benthic community.

Predicting biodiversity effects on ecosystem functioning requires adequate evaluation of the mechanisms explaining why more diverse systems could perform better than less diverse ones. In this context, tackling functional diversity has become an important issue. Even though the aggregation of species into functional groups supposes niche differences among groups, the concept of niche has not been fully exploited in the context of the biodiversity—ecosystem functioning research. Here we report the results of microcosm experiments where we used bacteria as a model to explore whether niche differences among species provide a good estimation of community functioning. For that we used experimental communities of denitrifying bacterial species and investigated the effects of bacterial diversity on two community processes, denitrification and anaerobic CO₂-production. We first measured the activities of 16 bacterial species grown individually on six different carbon sources. We then used the same set of species to assemble communities varying in both species richness and composition in microcosms containing a mixture of all six carbon sources. The performances of individual species on individual carbon sources were used to calculate, for each process measured, an a priori index called \"community niche\" that accounted for the performances of the species present in a given community across the entire range of the six resources. We found that species richness had a positive but small effect on both community processes whereas community niche explained a much larger proportion of the variation. According to the results of a path analysis, community niche was the main driver for the corresponding community process, but species richness affected community niche and thus had an indirect effect on denitrification and CO₂ production. In addition to community niche, the presence of particular bacterial species also influenced community functioning, indicating that other effects than the capacity to use carbon sources played a, albeit minor, role in our experiment. Our study provides evidence for the importance of resource niches in shaping biodiversity—ecosystem functioning relationships of bacterial communities.

Plant mutualistic association with various beneficial microbes is referred to as the plant enhancer microbiome. These microbes are found either in episphere or endosphere of the plant tissues. Several pieces of evidence have highlighted that plant microbiomes and soil play a pivotal role in making soil nutrient balance which is readily available to plants and provide strength under various stresses. Recently different technologies relevant to plant microbiome and diversity such as sequencing technologies, metagenomics, and bioinformatics have been utilized. Knowledge about factors that shape the composition of plant microbes is still less explored. Here, current insights into the issues driving the above/below plant microbial diversities are explored. Primarily, we address the distribution of microbial communities above and below ground across plant habitats that has benefitted plants. Microbial communities are efficient regulators of biogeochemical cycle which is a better approach to mitigate changing climatic patterns aids in proper utilization of greenhouse gases for their metabolic mechanisms. The present review is thereby significant for assessing microbiome mitigation toward climate change and multiple avenues of plant- microbe interaction under commuting climatic scenario. Finally, we summarize factors that promote the structure and composition of the plant microbiome.

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.