Opposing community assembly patterns for dominant and non-dominant plant species in herbaceous ecosystems globally

Dominant and non-dominant plants could be subject to different biotic and abiotic influences, partially because dominant plants modify the environment where non-dominant plants grow, causing an interaction asymmetry. Among other possibilities, if dominant plants compete strongly, they should deplete most resources forcing non-dominant plants into a more constrained niche space. Conversely, if dominant plants are constrained by the environment, they might not fully deplete available resources but instead ameliorate some of the environmental constraints limiting non-dominants. Hence, the nature of the interactions between the non-dominants could be modified by dominant species. However, when plant competition and environmental constraints have similar effects on dominant and non-dominant species no difference is expected. By estimating phylogenetic dispersion in 78 grasslands across five continents, we found that dominant species were clustered (underdispersed), suggesting dominant species are likely organized by environmental filtering, and that non-dominant species were either randomly assembled or overdispersed. Traits showed similar trends, but insufficient data prevented further analyses. Furthermore, several lineages scattered in the phylogeny had more non-dominant species, suggesting that traits related to non-dominants are phylogenetically conserved and have evolved multiple times. We found some environmental drivers of the dominant—non-dominant disparity. Our results indicate that assembly patterns for dominants and non-dominants are different, consistent with asymmetries in assembly mechanisms. Among the different mechanisms we evaluated, the results suggest two complementary hypotheses seldom explored: (1) Non-dominant species include lineages adapted to thrive in the environment generated by the dominant species. (2) Even when dominant species reduce resources to non-dominant ones, dominant species could have a stronger effect on—at least—some non-dominants by ameliorating the impact of the environment on them, than by depleting resources and increasing the environmental stress to those non-dominants. The results show that the dominant–non-dominant asymmetry has ecological and evolutionary consequences fundamental to understand plant communities.

Mobilization of antibiotic resistance genes differ by resistance mechanism

The degree to which antibiotic resistance genes (ARGs) are mobilized by insertion sequence (IS) elements, plasmids, and integrons has a strong association with their likelihood to function as resistance determinants. This stems from genetic decontextualization where strong promoters often present in IS elements and integrons and the copy number effect of plasmids contribute to high expression of accessory genes. Here, we screen all complete bacterial RefSeq genomes for ARGs. The genetic contexts of detected ARGs are investigated for IS elements, integrons, plasmids, and phylogenetic dispersion. The ARG-MOB scale is proposed which indicates how mobilized detected ARGs are in bacterial genomes. Antibiotic efflux genes are rarely mobilized and it is concluded that these are often housekeeping genes that are not decontextualized to confer resistance through overexpression. Even 80% of β-lactamases have never, or very rarely, been mobilized in the 15,790 studied genomes. However, some ARGs are indeed mobilized and co-occur with IS elements, plasmids, and integrons. These results have consequences for the design and interpretation of studies screening for resistance determinants, as mobilized ARGs pose a more concrete risk to human health, especially under heterologous expression, than groups of ARGs that have only been shown to confer resistance in cloning experiments.

Phylogenetic dispersion and diversity in regional assemblages of seed plants in China

Species assemble into communities through ecological and evolutionary processes. Phylogenetic niche conservatism—the tendency of species to retain ancestral ecological distributions—is thought to influence which species from a regional species pool can persist in a particular environment. We analyzed data for seed plants in China to test hypotheses about the distribution of species within regional floras. Of 16 environmental variables, actual evapotranspiration, minimum temperature of the coldest month, and annual precipitation most strongly influenced regional species richness, phylogenetic dispersion, and phylogenetic diversity for both gymnosperms (cone-bearing plants) and angiosperms (flowering plants). For most evolutionary clades at, and above, the family level, the relationships between metrics of phylogenetic dispersion (i.e., average phylogenetic distance among species), or phylogenetic diversity, and the 3 environmental variables were consistent with the tropical niche conservatism hypothesis, which predicts closer phylogenetic relatedness and reduced phylogenetic diversity with increasing environmental stress. The slopes of the relationships between phylogenetic relatedness and the 3 environmental drivers identified in this analysis were steeper for primarily tropical clades, implying greater niche conservatism, than for primarily temperate clades. These observations suggest that the distributions of seed plants across large-scale environmental gradients in China are constrained by conserved adaptations to the physical environment, i.e., phylogenetic niche conservatism.

Geophysical, evolutionary and ecological processes interact to drive phylogenetic dispersion in angiosperm assemblages along the longest elevational gradient in the world

Ecologists have embraced phylogenetic measures of assemblage structure, in large part for the promise of better mechanistic inferences. However, phylogenetic structure is driven by a wide array of factors from local biotic interactions to biogeographical history, complicating the mechanistic interpretation of a pattern. This may be particularly problematic along elevational gradients, where rapidly changing physical and biological conditions overlap with geological and biogeographical history, potentially producing complex patterns of phylogenetic dispersion (relatedness). We focus on the longest elevational gradient of vegetation in the world (i.e. c. 6000 m in Nepal) to explore patterns of phylogenetic dispersion for angiosperms (flowering plants) along this elevational gradient. We used the net relatedness index to quantify phylogenetic dispersion for each elevational band of 100 m. We found a zig-zag pattern of phylogenetic dispersion along this elevational gradient. With increasing elevation, the phylogenetic relatedness of species decreased for the elevational segment between 0 and c. 2100 m, increased for the elevational segment between 2100 and c. 4200 m, and decreased for the elevational segment above c. 4200 m. We consider this pattern to be a result of the interaction of geophysical (e.g. plate tectonics) and eco-evolutionary processes (e.g. niche conservatism and trait convergence). We speculate on the mechanisms that might have generated this zig-zag pattern of phylogenetic dispersion.

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes

BackgroundAssembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes.MethodsWe employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms.ResultsThe unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition.DiscussionVariation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space.

Root-colonizing and soil-borne communities of arbuscular mycorrhizal fungi in a temperate forest understorey

We analyzed arbuscular mycorrhizal fungal (AMF) communities in plant root samples from a natural forest ecosystem — a primeval forest in Järvselja, Estonia. AMF small-subunit (SSU) ribosomal RNA genes were subjected to 454-pyrosequencing and BLAST-based taxonomic identification. Seventy-six AMF sequence groups (virtual taxa, VT) were identified from plant roots. Taken together with seven additional VT recorded in an earlier investigation of soil AMF communities at the site, this represents the highest number of AMF reported from a single ecosystem to date. The six study plant species hosted similar AMF communities. However, AMF community composition in plant roots was significantly different from that in soil and considerably more VT were retrieved from roots than from soil. AMF VT identified from plant roots as a whole and from individual plant species were frequently phylogenetically clustered compared with local and global taxon pools, suggesting that nonrandom assembly processes, notably habitat filtering, may have shaped fungal assemblages. In contrast, the phylogenetic dispersion of AMF communities in soil did not differ from random subsets of the local or global taxon pools.