Elk, sagebrush, and saprotrophs: indirect top-down control on microbial community composition and function

Strong above-ground impacts of a non-native ungulate do not cascade to impact below-ground functioning in a boreal ecosystem

1. Experimental studies across biomes demonstrate that herbivores can have significant effects on ecosystem functioning. Herbivore effects, however, can be highly variable with studies demonstrating positive, neutral or negative relationships between herbivore presence and different components of ecosystems. Mixed effects are especially likely in the soil, where herbivore effects are largely indirect mediated through effects on plants. 2. We conducted a long-term experiment to disentangle the effects of non-native moose in boreal forests on plant communities, nutrient cycling, soil composition and soil organism communities. 3. To explore the effect of moose on soils, we conduct separate analyses on the soil organic and mineral horizons. Our data come from 11 paired exclosure-control plots in eastern and central Newfoundland, Canada that provide insight into 22-25 years of moose herbivory. We fit piecewise structural equations models (SEM) to data for the organic and mineral soil horizons to test different pathways linking moose to above-ground and below-ground functioning. 4. The SEMs revealed that moose exclusion had direct positive impacts on adult tree count and an indirect negative impact on shrub percent cover mediated by adult tree count. We detected no significant impact of moose on soil microbial C:N ratio or net nitrogen mineralization in the organic or mineral soil horizon. Soil temperature and moisture, however, was more than twice as variable in the presence (i.e. control) than absence (i.e. exclosure) of moose. Overall, we observed clear impacts of moose on above-ground forest components with limited indirect effects below-ground. Even after 22-25 years of exclusion, we did not find any evidence of moose impacts on soil microbial C:N ratio and net nitrogen mineralization. 5. Our long-term study and mechanistic path analysis demonstrates that soils can be resilient to ungulate herbivore effects despite evidence of strong effects above-ground. Long-term studies and analyses such as this one are relatively rare yet critical for reconciling some of the context-dependency observed across studies of ungulates effects on ecosystem functions. Such studies may be particularly valuable in ecosystems with short growing seasons such as the boreal forest.

Fungivorous nematodes drive microbial diversity and carbon cycling in soil

Soil bacteria and fungi mediate terrestrial biogeochemical cycling, but we know relatively little about how trophic interactions influence their community composition, diversity, and function. Specifically, it is unclear how consumer populations affect the activity of microbial taxa they consume, and therefore the interaction of those taxa with other members of the microbial community. Due to its extreme diversity, studying trophic dynamics in soil is a complex feat. Seeking to address these challenges, we performed a microcosm-based consumer manipulation experiment to determine the impact of a common fungal-feeding nematode (Aphelenchus avenae) on soil microbial community composition, diversity, and activity (e.g., C cycling parameters). Fungivory decreased fungal and bacterial α-diversity and stimulated C and N cycling, possibly via cascading impacts of fungivory on bacterial communities. Our results present experimental evidence that soil trophic dynamics are intimately linked with microbial diversity and function, factors that are key in understanding global patterns in biogeochemical cycling.

Unraveling the roles of genotype and environment in the expression of plant defense phenotypes

Phenotypic variability results from interactions between genotype and environment and is a major driver of ecological and evolutionary interactions. Measuring the relative contributions of genetic variation, the environment, and their interaction to phenotypic variation remains a fundamental goal of evolutionary ecology.In this study, we assess the question: How do genetic variation and local environmental conditions interact to influence phenotype within a single population? We explored this question using seed from a single population of common milkweed, Asclepias syriaca, in northern Michigan. We first measured resistance and resistance traits of 14 maternal lines in two common garden experiments (field and greenhouse) to detect genetic variation within the population. We carried out a reciprocal transplant experiment with three of these maternal lines to assess effects of local environment on phenotype. Finally, we compared the phenotypic traits measured in our experiments with the phenotypic traits of the naturally growing maternal genets to be able to compare relative effect of genetic and environmental variation on naturally occurring phenotypic variation. We measured defoliation levels, arthropod abundances, foliar cardenolide concentrations, foliar latex exudation, foliar carbon and nitrogen concentrations, and plant growth.We found a striking lack of correlation in trait expression of the maternal lines between the common gardens, or between the common gardens and the naturally growing maternal genets, suggesting that environment plays a larger role in phenotypic trait variation of this population. We found evidence of significant genotype-by-environment interactions for all traits except foliar concentrations of nitrogen and cardenolide. Milkweed resistance to chewing herbivores was associated more strongly with the growing environment. We observed no variation in foliar cardenolide concentrations among maternal lines but did observe variation among maternal lines in foliar latex exudation.Overall, our data reveal powerful genotype-by-environment interactions on the expression of most resistance traits in milkweed.

Soil microbial succession following surface mining is governed primarily by deterministic factors

Understanding the successional dynamics governing soil microbial community assembly following disturbance can aid in developing remediation strategies for disturbed land. However, the influences shaping microbial communities during succession following soil disturbance remain only partially understood. One example of a severe disturbance to soil is surface mining for natural resources, which displaces communities and changes the physical and chemical soil environment. These changes may alter community composition through selective pressure on microbial taxa (i.e. deterministic processes). Dispersal and ecological drift may also shape communities following disturbance (i.e. stochastic processes). Here, the relative influence of stochastic and deterministic processes on microbial community succession was investigated using a chronosequence of reclaimed surface mines ranging from 2-32 years post-reclamation. Sequencing of bacterial and fungal ribosomal gene amplicons coupled with a linear modeling approach revealed that following mine reclamation, while bacterial communities are modestly influenced by stochastic factors, the influence of deterministic factors was ∼7 × greater. Fungal communities were influenced only by deterministic factors. Soil organic matter, texture, and pH emerged as the most influential environmental factors on both bacterial and fungal communities. Our results suggest that management of deterministic soil characteristics over a sufficient time period could increase the microbial diversity and productivity of mine soils.

Environment-host-microbial interactions shape the Sarracenia purpurea microbiome at the continental scale

The importance of climate, habitat structure, and higher trophic levels on microbial diversity is only beginning to be understood. Here, we examined the influence of climate variables, plant morphology, and the abundance of aquatic invertebrates on the microbial biodiversity of the northern pitcher plant Sarracenia purpurea. The plant's cup-shaped leaves fill with rainwater and support a miniature, yet full-fledged, ecosystem with a diverse microbiome that decomposes captured prey and a small network of shredding and filter-feeding aquatic invertebrates that feed on microbes. We characterized pitcher microbiomes of 108 plants sampled at 36 sites from Florida to Quebec. Structural equation models revealed that annual precipitation and temperature, plant size, and midge abundance had direct effects on microbiome taxonomic and phylogenetic diversity. Climate variables also exerted indirect effects through plant size and midge abundance. Further, spatial structure and climate influenced taxonomic composition, but not phylogenetic composition. Our results suggest that direct effects of midge abundance and climate and indirect effects of climate through its effect on plant-associated factors lead to greater richness of microbial phylotypes in warmer, wetter sites.

Soil microbial communities and elk foraging intensity: implications for soil biogeochemical cycling in the sagebrush steppe

Foraging intensity of large herbivores may exert an indirect top-down ecological force on soil microbial communities via changes in plant litter inputs. We investigated the responses of the soil microbial community to elk (Cervus elaphus) winter range occupancy across a long-term foraging exclusion experiment in the sagebrush steppe of the North American Rocky Mountains, combining phylogenetic analysis of fungi and bacteria with shotgun metagenomics and extracellular enzyme assays. Winter foraging intensity was associated with reduced bacterial richness and increasingly distinct bacterial communities. Although fungal communities did not respond linearly to foraging intensity, a greater β-diversity response to winter foraging exclusion was observed. Furthermore, winter foraging exclusion increased soil cellulolytic and hemicellulolytic enzyme potential and higher foraging intensity reduced chitinolytic gene abundance. Thus, future changes in winter range occupancy may shape biogeochemical processes via shifts in microbial communities and subsequent changes to their physiological capacities to cycle soil C and N.