Species richness and trophic diversity increase decomposition in a co-evolved food web

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.

Prey identity affects fitness of a generalist consumer in a brown food web

The use of ever-advancing sequencing technologies has revealed incredible biodiversity at the microbial scale, and yet we know little about the ecological interactions in these communities. For example, in the phytotelmic community found in the purple pitcher plant, Sarracenia purpurea, ecologists typically consider the bacteria as a functionally homogenous group. In this food web, bacteria decompose detritus and are consumed by protozoa that are considered generalist consumers. Here, we tested whether a generalist consumer benefits from all bacteria equally. We isolated and identified 22 strains of bacteria, belonging to six genera, from S. purpurea plants. We grew the protozoa, Tetrahymena sp. with single isolates and strain mixtures of bacteria and measured Tetrahymena fitness. We found that different bacterial strains had different effects on protozoan fitness, both in isolation and in mixture. Our results demonstrate that not accounting for the composition of prey communities may affect the predicted outcome of predator-prey interactions.

Exploring Microbiome Functional Dynamics through Space and Time with Trait-Based Theory

Microbiomes play essential roles in the health and function of animal and plant hosts and drive nutrient cycling across ecosystems. Integrating novel trait-based approaches with ecological theory can facilitate the prediction of microbial functional traits important for ecosystem functioning and health. In particular, the yield-acquisition-stress (Y-A-S) framework considers dominant microbial life history strategies across gradients of resource availability and stress. However, microbiomes are dynamic, and spatial and temporal shifts in taxonomic and trait composition can affect ecosystem functions. We posit that extending the Y-A-S framework to microbiomes during succession and across biogeographic gradients can lead to generalizable rules for how microbiomes and their functions respond to resources and stress across space, time, and diverse ecosystems. We demonstrate the potential of this framework by applying it to the microbiomes hosted by the carnivorous pitcher plant Sarracenia purpurea, which have clear successional trajectories and are distributed across a broad climatic gradient.

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.

Trophic diversity and carbon sources supporting fish communities along a pollution gradient in a tropical river

Anthropogenic activities can have a great influence on water quality and in the availability of habitat and food resources, which can promote changes in the trophic diversity and carbon sources sustaining aquatic communities. The objective of this study was to evaluate if the trophic diversity and the main carbon sources sustaining fish communities change along a pollution gradient. The study was carried out at eight sites distributed along the Rio das Velhas, a Brazilian river highly impacted by anthropogenic activities, in which the discharge of domestic and industrial sewage from the Metropolitan Region of Belo Horizonte (MRBH) presents a major source of pollution. Using carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope ratios, we identified the major carbon sources/food sources of common fish species and calculated six metrics of trophic diversity. Autochthonous primary producers (algae, periphyton, and macrophytes) were the main carbon sources for all trophic guilds at all sites, but notably, sewage-derived organic matter was an additional significant carbon source to the fish community in the most polluted testing site. Here, the community was composed mainly by detritivorous and omnivorous fishes and exhibited greater ranges of carbon and nitrogen isotopic values, large total areas, high trophic diversity, small trophic redundancy, and less even distribution of trophic niches than the less polluted sites. We conclude that the trophic guilds, trophic diversity metrics, and carbon sources sustaining fish communities in the Rio das Velhas are highly influenced by the presence of pollution. Besides favoring omnivorous and detritivorous fishes, the input of sewage also provided an important food source to sustain the fish community from sites close to the MRBH.

Metabolic Functional Community Diversity of Associated Bacteria during the Degradation of Phytoplankton from a Drinking Water Reservoir

In the drinking water reservoir ecosystem, phytoplankton and bacteria play important roles in shaping freshwater health and function. In this work, the associated bacterial community functional diversity during degradation of phytoplankton was determined using the substrate utilization profiling (BIOLOG) technique, meanwhile, the composition and concentration of phytoplankton were examined using a microscope. The results indicated that Euglena decreased 58.33% from 0 to 38 d, while the smallest degradation of Bacillariophyta was 20.19%. Average well color development (AWCD_590nm) increased during the static periods from 0 to 38 d; however, the AWCD_590nm of 18 and 38 d had no significant difference (p < 0.05). The Simpson’s index (D) was in accordance with Shannon’s diversity (H) and species richness(S); it was measured to be18 > 38 > 5 > 0 d. There were significant differences in the pattern and level of carbon sources used by the phytoplankton-associated bacteria. In addition, the principle component analyses (PCA) suggested that the first principle component (PC1) and the second principle component (PC2) explained 46.76% and 21.49% of the total variation for bacterial community, respectively. Redundancy analysis (RDA) revealed that cell abundance of phytoplankton was negatively correlated with the AWCD_590nm, amino acids and other functional indexes. Therefore, the data suggest that there are differences in the phytoplankton-associated bacterial community functional diversity during different static stages of water samples collected from the drinking water reservoir.

Environmental correlates of food-chain length, mean trophic level and trophic level variance in invaded riverine fish assemblages

Examining how the trophic structure of biotic assemblages is affected by human impacts, such as habitat degradation and the introduction of alien species, is important for understanding the consequences of such impacts on ecosystem functioning. We used general linear mixed models and hierarchical partitioning analyses of variance to examine for the first time the applicability of three hypotheses (ecosystem-size, productivity and disturbance) for explaining food-chain length (FCL) in invaded fish assemblages. We used Fishbase trophic level (TL) estimates for 16 native and 18 alien fish species in an extensive riverine system in north-eastern Spain (99,700 km², 15 catchments, 530 sites). The FCL of assemblages ranged from 2.7 to 4.42. Ecosystem size-related variables (Strahler stream order, physical habitat diversity) and human-disturbance (conductivity) made the largest contribution to the explained variance in the FCL model after accounting for spatial confounding factors and collinearity among predictors. Within-assemblage TL also was positively associated with Strahler stream order, suggesting that large rivers have the highest trophic diversity. High conductivity was negatively associated with FCL, as did with the mean TL of fish assemblages. However, an inverse association was found between mean TL and Strahler stream order, possibly because the presence of fish species of high TL may be offset by larger numbers of alien species of lower TL in large rivers. Given that there may be trophic replacements among native and alien species, this inference needs to be addressed with detailed trophic studies. However, reducing water conductivity by improved wastewater treatment and better agricultural practices probably would help to conserve the fish species on the apices of aquatic food-webs.

Effects of grasshoppers on prairies: Herbivore composition matters more than richness in three grassland ecosystems

Understanding how biodiversity affects ecosystem processes is a key question in ecology. Previous research has found that increasing plant diversity often enhances many ecosystem processes, but less is known about the role of consumer diversity to ecosystem processes, especially in terrestrial ecosystems. Furthermore, we do not know how general biodiversity responses are among ecosystem types. We examined the role of insect herbivore (Orthoptera) diversity on plant production using parallel field experiments in three grassland ecosystems (mixed grass prairie, tallgrass prairie and coastal tallgrass prairie) to determine whether the effects of grasshopper diversity were consistent among sites. Using mesocosms, we manipulated orthopteran species richness (0, 1, 2, 3 or 4 species), functional richness (number of functional feeding groups present; 0, 1 or 2 functional groups) and functional composition (composition of functional groups present; mixed-feeders only, grass-feeders only, both mixed-feeders and grass-feeders). Diversity treatments were maintained throughout the experiment by replacing dead individuals. Plant biomass was destructively sampled at the end of the experiment. We found no effect of species richness or functional richness on plant biomass. However, herbivore functional composition was important, and effects were qualitatively similar across sites: The presence of only grass-feeding species reduced plant biomass more than either mixed-feeding species alone or both groups together. Orthopterans had consistent effects across a range of abiotic conditions, as well as different plant community and orthopteran community compositions. Our results suggest that functional composition of insect herbivores affects plant communities in grasslands more than herbivore species richness or functional richness, and this pattern was robust among grassland types.

Convergence between the microcosms of Southeast Asian and North American pitcher plants

The ‘pitchers’ of carnivorous pitcher plants are exquisite examples of convergent evolution. An open question is whether the living communities housed in pitchers also converge in structure or function. Using samples from more than 330 field-collected pitchers of eight species of Southeast Asian Nepenthes and six species of North American Sarracenia, we demonstrate that the pitcher microcosms, or miniature ecosystems with complex communities, are strikingly similar. Compared to communities from surrounding habitats, pitcher communities house fewer species. While communities associated with the two genera contain different microbial organisms and arthropods, the species are predominantly from the same phylogenetic clades. Microbiomes from both genera are enriched in degradation pathways and have high abundances of key degradation enzymes. Moreover, in a manipulative field experiment, Nepenthes pitchers placed in a North American bog assembled Sarracenia-like communities. An understanding of the convergent interactions in pitcher microcosms facilitates identification of selective pressures shaping the communities.

The ecosystems found across the Earth, including in forests, lakes and prairies, consist of communities of plants, animals and microbes. How these organisms interact with each other determines which ones grow and thrive. We still do not understand how communities form: why different species exist where they do, and what enables them to survive in different locations. This knowledge is particularly limited with regard to communities of microbes because they are hard to see and count.

Pitcher plants are an ideal system for studying how communities and ecosystems assemble. The pitcher-shaped leaves of these plants each contain small aquatic communities of microbes and arthropods (including insects and mites) that can be relatively easily studied. Because unrelated groups of plants have evolved pitchers at different times and on different continents, these communities can also be used to explore how evolutionary history and the current environment determine which species thrive in a particular location.

Bittleston et al. sampled the DNA of the communities living within 330 pitchers from various North American and Southeast Asian pitcher plant species. This revealed that very distantly related plants on opposite sides of the planet have pitchers that host similar communities, with the organisms found in one pitcher plant often closely related to the organisms found in others. The genes within the community’s DNA also shared many functions, with the majority of shared genes devoted to digesting captured insect prey. Bittleston et al. also relocated pitcher plants from Southeast Asia to grow alongside North American species and found the same microbes and arthropods colonizing both groups, indicating that the different types of pitchers present a similar habitat.

Overall, the results of the experiments performed by Bittleston et al. suggest that certain kinds of interactions between species (such as between the pitcher plants and their microbes) can evolve independently in different parts of the world. Researchers can use these interactions to learn more about how communities and ecosystems form. With a greater understanding of the Earth’s ecosystems, it will be easier to protect them and predict how they will fare as global conditions change.

Landscape variation influences trophic cascades in dengue vector food webs

The epidemiology of vector-borne diseases is governed by a structured array of correlative and causative factors, including landscape (for example, rural versus urban), abiotic (for example, weather), and biotic (for example, food web) factors. Studies of mosquito-borne diseases rarely address these multiple factors at large spatial scales, which limits insights into how human alterations of landscapes and food webs alter mosquito abundance. We used structural equation modeling to identify the relative magnitude and direction of landscape, abiotic, and food web factors on Aedes larvae and adults across 70 sites in northern Thailand. Food web factors were modeled as mosquito-predator trophic cascades. Landscape context affected mosquito-predator communities in aquatic and terrestrial environments via cascading food web interactions. Several mosquito predators within these food webs showed potential as biocontrol agents in mosquito population control, but their potentials for control were landscape-dependent. In terrestrial food webs, the habitat-sensitive tokay gecko structured mosquito-predator communities, indicating that a conservation approach to vector control could be a useful addition to existing control efforts.

The significance of linoleic acid in food sources for detritivorous benthic invertebrates

Chemical composition of organic matter (OM) is a key driver for detritus consumption by macroinvertebrates and polyunsaturated fatty acid (PUFA) content is considered a candidate indicator of food palatability. Since traditionally used complex natural OM covaries in many quality attributes, it remains uncertain whether benthic invertebrates developed an actual preference for PUFA-rich food. Therefore we aimed to test the influence of the PUFA linoleic acid on OM consumption by aquatic macroinvertebrates using standardized surrogate substrates (decomposition and consumption tablet, DECOTAB) with added linoleic acid (PUFA) in comparison to consumption of DECOTAB containing only cellulose (Standard) or ground macrophytes (Plant). In microcosms, we observed a higher consumption rate of PUFA DECOTAB in comparison to Standard DECOTAB in two functionally distinct invertebrate species (Lumbriculus variegatus and Asellus aquaticus). This effect appeared to be overruled in the field due to unknown sources of natural variation. Although we observed higher consumption rates in species-rich ditches compared to species-poor ditches, consumption rates were comparable for all three types of DECOTAB deployed. Upon reduced food quality and palatability, results presented here hint that PUFA like linoleic acid may be a key OM attribute driving the performance of benthic macroinvertebrates and inherent functioning of aquatic ecosystems.

Predator-driven elemental cycling: the impact of predation and risk effects on ecosystem stoichiometry

Empirical evidence is beginning to show that predators can be important drivers of elemental cycling within ecosystems by propagating indirect effects that determine the distribution of elements among trophic levels as well as determine the chemical content of organic matter that becomes decomposed by microbes. These indirect effects can be propagated by predator consumptive effects on prey, nonconsumptive (risk) effects, or a combination of both. Currently, there is insufficient theory to predict how such predator effects should propagate throughout ecosystems. We present here a theoretical framework for exploring predator effects on ecosystem elemental cycling to encourage further empirical quantification. We use a classic ecosystem trophic compartment model as a basis for our analyses but infuse principles from ecological stoichiometry into the analyses of elemental cycling. Using a combined analytical-numerical approach, we compare how predators affect cycling through consumptive effects in which they control the flux of nutrients up trophic chains; through risk effects in which they change the homeostatic elemental balance of herbivore prey which accordingly changes the element ratio herbivores select from plants; and through a combination of both effects. Our analysis reveals that predators can have quantitatively important effects on elemental cycling, relative to a model formalism that excludes predator effects. Furthermore, the feedbacks due to predator nonconsumptive effects often have the quantitatively strongest impact on whole ecosystem elemental stocks, production and efficiency rates, and recycling fluxes by changing the stoichiometric balance of all trophic levels. Our modeling framework predictably shows how bottom-up control by microbes and top-down control by predators on ecosystems become interdependent when top predator effects permeate ecosystems.

Microbial community structure of a pilot-scale thermophilic anaerobic digester treating poultry litter

The microbial community structure of a stable pilot-scale thermophilic continuous stirred tank reactor digester stabilized on poultry litter was investigated. This 40-m(3) digester produced biogas with 57% methane, and chemical oxygen demand removal of 54%. Bacterial and archaeal diversity were examined using both cloning and pyrosequencing that targeted 16S rRNA genes. The bacterial community was dominated by phylum Firmicutes, constituting 93% of the clones and 76% of the pyrotags. Of the Firmicutes, class Clostridia (52% pyrotags) was most abundant followed by class Bacilli (13% pyrotags). The bacterial libraries identified 94 operational taxonomic units (OTUs) and pyrosequencing identified 577 OTUs at the 97% minimum similarity level. Fifteen OTUs were dominant (≥2% abundance), and nine of these were novel unclassified Firmicutes. Several of the dominant OTUs could not be classified more specifically than Clostridiales, but were most similar to plant biomass degraders, including Clostridium thermocellum. Of the rare pyrotag OTUs (<0.5% abundance), 75% were Firmicutes. The dominant methanogen was Methanothermobacter which has hydrogenotrophic metabolism, and accounted for >99% of the archaeal clones. Based on the primary methanogen, as well as digester chemistry (high VA and ammonia levels), we propose that bacterial acetate oxidation is the primary pathway in this digester for the control of acetate levels.

Organic-matter loading determines regime shifts and alternative states in an aquatic ecosystem

Slow changes in underlying state variables can lead to "tipping points," rapid transitions between alternative states ("regime shifts") in a wide range of complex systems. Tipping points and regime shifts routinely are documented retrospectively in long time series of observational data. Experimental induction of tipping points and regime shifts is rare, but could lead to new methods for detecting impending tipping points and forestalling regime shifts. By using controlled additions of detrital organic matter (dried, ground arthropod prey), we experimentally induced a shift from aerobic to anaerobic states in a miniature aquatic ecosystem: the self-contained pools that form in leaves of the carnivorous northern pitcher plant, Sarracenia purpurea. In unfed controls, the concentration of dissolved oxygen ([O2]) in all replicates exhibited regular diurnal cycles associated with daytime photosynthesis and nocturnal plant respiration. In low prey-addition treatments, the regular diurnal cycles of [O2] were disrupted, but a regime shift was not detected. In high prey-addition treatments, the variance of the [O2] time series increased until the system tipped from an aerobic to an anaerobic state. In these treatments, replicate [O2] time series predictably crossed a tipping point at ~45 h as [O2] was decoupled from diurnal cycles of photosynthesis and respiration. Increasing organic-matter loading led to predictable changes in [O2] dynamics, with high loading consistently driving the system past a well-defined tipping point. The Sarracenia microecosystem functions as a tractable experimental system in which to explore the forecasting and management of tipping points and alternative regimes.

The dissimilarity of species interaction networks

In a context of global changes, and amidst the perpetual modification of community structure undergone by most natural ecosystems, it is more important than ever to understand how species interactions vary through space and time. The integration of biogeography and network theory will yield important results and further our understanding of species interactions. It has, however, been hampered so far by the difficulty to quantify variation among interaction networks. Here, we propose a general framework to study the dissimilarity of species interaction networks over time, space or environments, allowing both the use of quantitative and qualitative data. We decompose network dissimilarity into interactions and species turnover components, so that it is immediately comparable to common measures of β-diversity. We emphasise that scaling up β-diversity of community composition to the β-diversity of interactions requires only a small methodological step, which we foresee will help empiricists adopt this method. We illustrate the framework with a large dataset of hosts and parasites interactions and highlight other possible usages. We discuss a research agenda towards a biogeographical theory of species interactions.

Detritus quality controls macrophyte decomposition under different nutrient concentrations in a eutrophic shallow lake, North China

Macrophyte decomposition is important for carbon and nutrient cycling in lake ecosystems. Currently, little is known about how this process responds to detritus quality and water nutrient conditions in eutrophic shallow lakes in which incomplete decomposition of detritus accelerates the lake terrestrialization process. In this study, we investigated the effects of detritus quality and water nutrient concentrations on macrophyte decomposition in Lake Baiyangdian, China, by analyzing the decomposition of three major aquatic plants at three sites with different pollution intensities (low, medium, and high pollution sites). Detritus quality refers to detritus nutrient contents as well as C∶N, C∶P, and N∶P mass ratios in this study. Effects of detritus mixtures were tested by combining pairs of representative macrophytes at ratios of 75∶25, 50∶50 and 25∶75 (mass basis). The results indicate that the influence of species types on decomposition was stronger than that of site conditions. Correlation analysis showed that mass losses at the end of the experimental period were significantly controlled by initial detritus chemistry, especially by the initial phosphorus (P) content, carbon to nitrogen (C∶N), and carbon to phosphorus (C∶P) mass ratios in the detritus. The decomposition processes were also influenced by water chemistry. The NO₃-N and NH₄-N concentrations in the lake water retarded detritus mass loss at the low and high pollution sites, respectively. Net P mineralization in detritus was observed at all sites and detritus P release at the high pollution site was slower than at the other two sites. Nonadditive effects of mixtures tended to be species specific due to the different nutrient contents in each species. Results suggest that the nonadditive effects varied significantly among different sites, indicating that interactions between the detritus quality in species mixtures and site water chemistry may be another driver controlling decomposition in eutrophic shallow lakes.