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This study focused on the legacy effects of 8-year application of N (in gradient of 0, 140, 280, 470, and 660 kg N ha−1 year−1) on the bacterial community diversity, interactions, and assembly processes in the wheat rhizosphere. The rhizosphere bacterial α-diversity increased with the rate of historical N input, while it did not change at N addition rates of over 280 kg N ha−1 year−1. Historical N input clearly shifted the rhizosphere bacterial community composition, and soils with more N input were more dissimilar to those without N input. The net relatedness index (NRI) and nearest taxon index (NTI) analysis revealed that the rhizosphere bacterial communities in most samples were phylogenetically clustered, and the treatments with high N (> 470 kg N ha−1 year−1) showed higher levels of clustering than those with low N (< 140 kg N ha−1 year−1), indicating more environmental selection stress in soil with higher historical N input. Increased co-occurrence network size and connectivity were accompanied by increased aboveground biomass of wheat. Overall, with the increase in historical N input, the resulting legacy effects forced the bacterial community in the rhizosphere to undergo higher environmental selection pressure, and indirectly affected the complexity of wheat rhizosphere assemblages during subsequent crop growth.

As a key microbial community component with important ecological roles, archaea merit the attention of biologists and ecologists. The mechanisms controlling microbial community diversity, composition, and biogeography are central to microbial ecology but poorly understood. Archaea are a major part of Earth’s life. They are believed to play important roles in nutrient biogeochemical cycling in the mangrove. However, only a few studies on the archaeal community in mangroves have been reported. In particular, the assembly processes and interaction patterns that impact the archaeal communities in mangroves have not been investigated to date. Here, the biogeography, assembly patterns, and driving factors of archaeal communities in seven representative mangroves across southeastern China were systematically analyzed. The analysis revealed that the archaeal community is more diverse in surface sediments than in subsurface sediments, and more diverse in mangroves at low latitudes than at high latitudes, with Woesearchaeota and Bathyarchaeota as the most diverse and most abundant phyla, respectively. Beta nearest-taxon index analysis suggested a determinant role of homogeneous selection on the overall archaeon community in all mangroves and in each individual mangrove. In addition, the conditionally rare taxon community was strongly shaped by homogeneous selection, while stochastic processes shaped the dominant taxon and always-rare taxon communities. Further, a moderate effect of environmental selection on the archaeal community was noted, with the smallest effect on the always-rare taxon community. Mangrove location, mean annual temperature, and salinity were the major factors that greatly affected the community composition. Finally, network analysis revealed comprehensive cooccurrence relationships in the archaeal community, with a crucial role of Bathyarchaeota . This study expands the understanding of the biogeography, assembly patterns, driving factors, and cooccurrence relationships of the mangrove archaeal community and inspires functional exploration of archaeal resources in mangrove sediments. IMPORTANCE As a key microbial community component with important ecological roles, archaea merit the attention of biologists and ecologists. The mechanisms controlling microbial community diversity, composition, and biogeography are central to microbial ecology but poorly understood. Mangroves are located at the land-ocean interface and are an ideal environment for examining the above questions. We here provided the first-ever overview of archaeal community structure and biogeography in mangroves located along an over-9,000-km coastline of southeastern China. We observed that archaeal diversity in low-latitude mangroves was higher than that in high-latitude mangroves. Furthermore, our data indicated that homogeneous selection strongly controlled the assembly of the overall and conditionally rare taxon communities in mangrove sediments, while the dominant taxon and always-rare taxon communities were mainly controlled by dispersal limitation.

The community composition of any group of organisms should theoretically be determined by a combination of assembly processes including resource partitioning, competition, environmental filtering, and phylogenetic legacy. Environmental DNA studies have revealed a huge diversity of protists in all environments, raising questions about the ecological significance of such diversity and the degree to which they obey to the same rules as macroscopic organisms. The fast‐growing cultivable protist species on which hypotheses are usually experimentally tested represent only a minority of the protist diversity. Addressing these questions for the lesser known majority can only be inferred through observational studies. We conducted an environmental DNA survey of the genus Nebela, a group of closely related testate (shelled) amoeba species, in different habitats within Sphagnum‐dominated peatlands. Identification based on the mitochondrial cytochrome c oxidase 1 gene, allowed species‐level resolution as well as phylogenetic reconstruction. Community composition varied strongly across habitats and associated environmental gradients. Species showed little overlap in their realized niche, suggesting resource partitioning, and a strong influence of environmental filtering driving community composition. Furthermore, phylogenetic clustering was observed in the most nitrogen‐poor samples, supporting phylogenetic inheritance of adaptations in the group of N. guttata. This study showed that the studied free‐living unicellular eukaryotes follow to community assembly rules similar to those known to determine plant and animal communities; the same may be true for much of the huge functional and taxonomic diversity of protists.

Taxa co‐occurring in communities often represent a nonrandom sample, in phenotypic or phylogenetic terms, of the regional species pool. While heuristic arguments have identified processes that create community phylogenetic patterns, further progress hinges on a more comprehensive understanding of the interactions between underlying ecological and evolutionary processes. We created a simulation framework to model trait evolution, assemble communities (via competition, habitat filtering, or neutral assembly), and test the phylogenetic pattern of the resulting communities. We found that phylogenetic community structure is greatest when traits are highly conserved and when multiple traits influence species membership in communities. Habitat filtering produces stronger phylogenetic structure when taxa with derived (as opposed to ancestral) traits are favored in the community. Nearest‐relative tests have greater power to detect patterns due to competition, while total community relatedness tests perform better with habitat filtering. The size of the local community relative to the regional pool strongly influences statistical power; in general, power increases with larger pool sizes for communities created by filtering but decreases for communities created by competition. Our results deepen our understanding of processes that contribute to phylogenetic community structure and provide guidance for the design and interpretation of empirical research.

In 2009, a derecho occurred in southern Illinois, affecting large areas of the regional forest systems. Previous research reported multi-strata species compositional shifts post-derecho at LaRue Pine Hills/Otter Pond Research Natural Area but did not investigate how these changes varied within the RNA. These observations are expanded here to include phylogenetic and spatial relationships to show how compositional shifts can vary within a landscape. Surveys were conducted the year before and after the derecho. Univariate and multivariate analyses identified elevation as an environmental driver of diversity and community composition. Spatial analyses identified spatial patterns in taxonomic (TSR) and phylogenetic (PSR) species richness, and metrics of phylogenetic clustering and overdispersion (net relatedness index and nearest taxon index; NRI and NTI, respectively), in seedling, sapling, and tree communities. Tree TSR and PSR and sapling PSR decreases and sapling NTI increases occurred post-derecho. Seedling diversity-elevational relationships exhibited humped-backed relationships, while saplings showed positive linear relationships between phylogenetic metrics and elevation. Local Moran’s I analysis showed post-derecho clustering in the north-central extent for seedling, sapling, and tree strata. Co-Kriging interpolation predicted seedling diversity increases in the southwestern extent, with sapling and tree diversity increases in the eastern extent and the north-central extent respectively post-derecho, indicating competitive interactions at lower elevations and environmental filtering at higher elevations. Seedling and tree NRI and NTI increased in the southern extent, whereas sapling clustering increased in the northeastern extent. These relationships indicate how community assembly processes (i.e., competition or environmental filtering) are altered following large-scale disturbance.

AIM: Ecologists have long been concerned with understanding how local communities are assembled from the pool of species present in the broader biogeographical region. Although there has been considerable interest in the use of measures of species relatedness as tools to detect community assembly process, empirical and simulation studies have produced mixed results on the effectiveness of the technique. Here, we ask how well the most commonly used metrics of such community phylogenetic patterns detect the operation of filtering and competition in simulated communities where filtering and competition determine species abundances as well as co‐occurrence patterns. LOCATION: Simulated local communities assembled from a simulated regional species pool. METHODS: We simulate the evolution of niche traits for a regional species pool on a phylogeny, and then simulate the assembly of a local community from this regional species pool using a Lotka–Volterra model. We then test whether the net relatedness index (NRI) or the nearest taxon index (NTI) can detect the assembly process. We compare the performance of abundance‐weighted (NRIAW and NTIAW) and occurrence‐based (NRIO and NTIO) versions of the metrics along a gradient of local community size as a percentage of the regional pool. RESULTS: We find that abundance weighting can substantially increase the power to detect assembly processes. Moreover, clustering and over‐dispersion are, in fact, most detectable when assembly processes act mainly on abundance rather than occurrence. Where they differed, NTIAW tended to outperform NRIAW at detecting limiting‐similarity competition. NRIAW outperformed NTIAW at detecting filtering except when filtering was very strong compared with limiting‐similarity competition. MAIN CONCLUSIONS: Our findings imply that phylogenetic information is more likely to yield information about community assembly when abundance information is incorporated, and local communities contain a relatively large fraction of the regional species pool.

Competition has long been proposed as an important force in structuring mammalian communities. Although early work recognized that competition has a phylogenetic dimension, only with recent increases in the availability of phylogenies have true phylogenetic investigations of mammalian community structure become possible. We test whether the phylogenetic structure of 142 assemblages from three mammalian clades (New World monkeys, North American ground squirrels and Australasian possums) shows the imprint of competition. The full set of assemblages display a highly significant tendency for members to be more distantly related than expected by chance (phylogenetic overdispersion). The overdispersion is also significant within two of the clades (monkeys and squirrels) separately. This is the first demonstration of widespread overdispersion in mammal assemblages and implies an important role for either competition between close relatives where traits are conserved, habitat filtering where distant relatives share convergent traits, or both.

Nitrogen (N) deposition rates have notably increased around the world, especially in high-altitude regions like the Qinghai–Tibetan Plateau (QTP). We conducted a six-year comprehensive experiment to simulate nitrogen deposition in an alpine grassland area near Qinghai Lake. Four levels of nitrogen depositions, i.e., 0 (CK), 8 kg N ha−1year−1 (N1), 40 kg N ha−1year−1 (N2), and 72 kg N ha−1year−1 (N3), with three replicates for each N treatment, were tested annually in early May and early July, with the meticulous collection of plant and soil samples during the peak growth period from 15 July to 15 August. We used the null model to evaluate the impact of environmental filtration and interspecific competition on the dynamics of the plant community was assessed based on the level of discrete species affinities within the plant community by constructing a phylogenetic tree. The results showed that the environmental filter was the predominant driver for the change of community’s genealogical fabric. The N2 and N3 treatments increased the influence of soil factors on the change of plant community structure. Climatic factors played a crucial role on the change of plant community in the CK grassland area, while soil factors were dominant in the N1- and N3-treated grasslands.

Prevention is the most effective way of mitigating the negative impacts of exotic species invasions on biodiversity. Preventative measures include inhibiting the further dispersal and recruitment of established invasive species. We expect coffee production in agroforestry systems to reduce the recruitment of exotic species relative to monoculture stands because intercropped trees function as environmental filters that select for individuals with traits such as shade tolerance. If ecologically similar species are also closely related phylogenetically, such environmental filters should reduce phylogenetic diversity, supporting the coexistence of closely related species. Here, we test whether the taxonomic and phylogenetic diversity of native and exotic species in agroforestry systems is lower than in monocultures. We sampled the understory in 180 plots distributed in both habitats in three study sites within the Araponga municipality, Brazil, and measured understory light availability. Phylogenetic diversity was calculated as the net relatedness index (NRI) and the nearest taxon index (NTI). Understory light availability was lower in agroforestry systems. Of the 48 species found, 25 occurred in agroforestry systems, three of which were exotics. Forty-two species were found in monoculture stands (including 13 exotics). As expected, NRI and NTI indicated lower phylogenetic diversity in agroforestry systems than in monoculture stands. Agroforestry systems provide less favorable habitats for exotic species, filtering them from the understory. The mechanisms that select against exotic species remain unknown; however, shading might exclude predominantly heliophytic exotic species from the agricultural matrix. Therefore, agroforestry systems may function as buffer zones preventing invasion into sensitive ecosystems.