Seasonal shifts in the importance of bottom–up and top–down factors on stream periphyton community structure

We examined the importance of temporal variability in top–down and bottom–up effects on the accumulation of stream periphyton, which are complex associations of autotrophic and heterotrophic microorganisms. Periphyton contributes to primary production and nutrient cycling and serves as a food resource for herbivores (grazers). Periphyton growth is often limited by the availability of nitrogen and phosphorus, and biomass can be controlled by grazers. In this study we experimentally manipulated nutrients and grazers simultaneously to determine the relative contribution of bottom–up and top–down controls on periphyton over time. We used nutrient diffusing substrates to regulate nutrient concentrations and an underwater electric field to exclude grazing insects in three sequential 16–17 day experiments from August to October in montane Colorado, USA. We measured algal biomass, periphyton organic mass, and algal community composition in each experiment and determined densities of streambed insect species, including grazers. Phosphorus was the primary limiting nutrient for algal biomass, but it did not influence periphyton organic mass across all experiments. Effects of nutrient additions on algal biomass and community composition decreased between August and October. Grazed substrates supported reduced periphyton biomass only in the first experiment, corresponding to high benthic abundances of a dominant mayfly grazer (Rhithrogena spp.). Grazed substrates in the first experiment also showed altered algal community composition with reduced diatom relative abundances, presumably in response to selective grazing. We showed that top–down grazing effects were strongest in late summer when grazers were abundant. The effects of phosphorus additions on algal biomass likely decreased over time because temperature became more limiting to growth than nutrients, and because reduced current velocity decreased nutrient uptake rates. These results suggest that investigators should proceed with caution when extending findings based on short‐term experiments. Furthermore, these results support the need for additional seasonal‐scale field research in stream ecology.     

Intraspecific and intergenerational differences in plant–soil feedbacks

Interactions between plant and soil communities are known to play an integral role in shaping ecosystems. Plants influence the composition of soil communities and soil communities in turn influence plant performance. Such a plant–soil feedback may incur selection pressure on plants and the associating soil community. However, the evolutionary consequences of these above–belowground feedback interactions remain largely speculative. Here we assess whether plant–soil feedback effects differ between intraspecific plant populations and between generations within the same plant population. We used two populations of Trifolium pratense and assessed their performance when grown in association with their home versus away soil biota. Both populations were colonized by distinct microbial communities and performed better with their own home soil communities than with the soil community from the other intraspecific population, demonstrating intraspecific positive feedback effects of home soil. In one of the two populations, we found that plant performance and the root associated microbiota community differed between parental and progeny plants when inoculated with their own home soil. Differences in root associated community characteristics could explain more than 80% of the variation in performance among the progeny and parental plants. Our results highlight that intraspecific differences in both plant and associated soil communities shape plant–soil feedback effects, and consequently indicate that plant–soil feedback can influence the direction of selection between intraspecific plant populations.     

The importance of interannual variation and bottom–up nitrogen enrichment for plant–pollinator networks

Striking changes in food web structure occur with alterations in resource supply. Like predator–prey interactions, many mutualisms are also consumer–resource interactions. However, no studies have explored how the structure of plant–pollinator networks may be affected by nutrient enrichment. For three years, we enriched plots of subalpine plant communities with nitrogen and observed subsequent effects on plant–pollinator network structure. Although nitrogen enrichment affects floral abundance and rates of pollinator visitation, we found no effects of nitrogen enrichment on the core group of generalist plants and pollinators or on plant–pollinator network structure parameters, such as network topology (the identity and frequency of interactions) and the degree of nestedness. However, individual plant and pollinator taxa were packed into the nested networks differently among nitrogen treatments. In particular, pollinators visited different numbers and types of plants in the nested networks, suggesting weak, widespread effects of nitrogen addition on individual taxa. Independent of nitrogen enrichment, there were large interannual differences in network structure and interactions, due to species turnover among years and flexibility in interacting with new partners. These data suggest that the community structure of small‐scale mutualistic networks may be relatively robust to short‐term bottom–up changes in the resource supply, but sensitive to variation in the opportunistic behavior and turnover of plant and pollinator species among years.     

Intraspecific phenotypic variation in a fish predator affects multitrophic lake metacommunity structure

Contemporary insights from evolutionary ecology suggest that population divergence in ecologically important traits within predators can generate diversifying ecological selection on local community structure. Many studies acknowledging these effects of intraspecific variation assume that local populations are situated in communities that are unconnected to similar communities within a shared region. Recent work from metacommunity ecology suggests that species dispersal among communities can also influence species diversity and composition but can depend upon the relative importance of the local environment. Here, we study the relative effects of intraspecific phenotypic variation in a fish predator and spatial processes related to plankton species dispersal on multitrophic lake plankton metacommunity structure. Intraspecific diversification in foraging traits and residence time of the planktivorous fish alewife (Alosa pseudoharengus) among coastal lakes yields lake metacommunities supporting three lake types which differ in the phenotype and incidence of alewife: lakes with anadromous, landlocked, or no alewives. In coastal lakes, plankton community composition was attributed to dispersal versus local environmental predictors, including intraspecific variation in alewives. Local and beta diversity of zooplankton and phytoplankton was additionally measured in response to intraspecific variation in alewives. Zooplankton communities were structured by species sorting, with a strong influence of intraspecific variation in A. pseudoharengus. Intraspecific variation altered zooplankton species richness and beta diversity, where lake communities with landlocked alewives exhibited intermediate richness between lakes with anadromous alewives and without alewives, and greater community similarity. Phytoplankton diversity, in contrast, was highest in lakes with landlocked alewives. The results indicate that plankton dispersal in the region supplied a migrant pool that was strongly structured by intraspecific variation in alewives. This is one of the first studies to demonstrate that intraspecific phenotypic variation in a predator can maintain contrasting patterns of multitrophic diversity in metacommunities.     

Meiofauna affect the macrobenthic biodiversity–ecosystem functioning relationship

The biodiversity–ecosystem functioning (B–EF) relationship has become of main interest in the last few decades, mostly because of the worldwide increase in species extinctions. However, most of these studies only consider species within single size‐class or trophic level, thereby most likely underestimating ecosystem complexity. To reach more realistic scenarios, we assessed the role of meiofauna (lower size‐class level) on the relationship between macrofaunal biodiversity and multiple benthic ecosystem properties. Experiments took place under controlled conditions using three macrofaunal species (Alitta (formerly Nereis) virens, Macoma balthica and Mya arenaria). A total of eight combinations of zero to three functionally different macrofaunal species were maintained in microcosms for 34 days in either the presence or absence of a different size‐class grouping (a meiofaunal mixture). The organic matter content and bacterial abundance in sediments and the oxygen and nutrient (NH₄⁺, NO_x^?, PO₄^3?) fluxes across the sediment‐water interface were measured and used as proxies of ecosystem properties. Overall, macrofaunal species richness did not modify any of the measured properties; however, we observed changes associated to the presence of A. virens and M. balthica. This study also revealed a strong impact of the presence of meiofauna on ecosystem properties. They changed interactions between macrofaunal species, which led to modifications in the ecosystem properties. Thus, even if this size‐class group has been poorly considered in previous studies, this experiment suggests that future studies should consider the meiofauna with greater attention, particularly in the context of B–EF.     

Climatic role of terrestrial ecosystem under elevated CO2: a bottom‐up greenhouse gases budget

The net balance of greenhouse gas (GHG) exchanges between terrestrial ecosystems and the atmosphere under elevated atmospheric carbon dioxide (CO₂) remains poorly understood. Here, we synthesise 1655 measurements from 169 published studies to assess GHGs budget of terrestrial ecosystems under elevated CO₂. We show that elevated CO₂ significantly stimulates plant C pool (NPP) by 20%, soil CO₂ fluxes by 24%, and methane (CH₄) fluxes by 34% from rice paddies and by 12% from natural wetlands, while it slightly decreases CH₄ uptake of upland soils by 3.8%. Elevated CO₂ causes insignificant increases in soil nitrous oxide (N₂O) fluxes (4.6%), soil organic C (4.3%) and N (3.6%) pools. The elevated CO₂‐induced increase in GHG emissions may decline with CO₂ enrichment levels. An elevated CO₂‐induced rise in soil CH₄ and N₂O emissions (2.76 Pg CO₂‐equivalent year^?1) could negate soil C enrichment (2.42 Pg CO₂ year^?1) or reduce mitigation potential of terrestrial net ecosystem production by as much as 69% (NEP, 3.99 Pg CO₂ year^?1) under elevated CO₂. Our analysis highlights that the capacity of terrestrial ecosystems to act as a sink to slow climate warming under elevated CO₂ might have been largely offset by its induced increases in soil GHGs source strength.     

Berry production drives bottom–up effects on body mass and reproductive success in an omnivore

Obligate herbivores dominate studies of the effects of climate change on mammals, however there is limited empirical evidence for how changes in the abundance or quality of plant food affect mammalian omnivores. Omnivores can exploit a range of different food resources over the course of a year, but they often rely on seasonally restricted highly nutritious fruiting bodies during critical life stages. Brown bears Ursus arctos in Sweden are dependent on berries for fattening before entering hibernation. We used a ten‐year time series to evaluate the effect of temperature and snow on annual variation in berry abundance and how this variation affected bears. We found marked interannual variation in berry production of bilberry Vaccinium myrtillus and lingonberry V. vitis‐idaea, that we could attribute in part to temperature during plant dormancy and flowering and precipitation during fruit ripening. Both, autumn weights of female bears and spring weights of yearling bears increased linearly with bilberry abundance. When bilberry abundance was low, lightweight female bears had a lower reproductive success than females in better condition. This effect vanished when food abundance was above average, indicating that lightweight females could compensate for their initial weight during good bilberry years. Our study highlights the importance of considering individuals’ dynamic responses to variation in food availability, which leave some more vulnerable to food shortage than others. Individual life‐history heterogeneity in response to resource variation likely affects long‐term population recruitment. Our findings emphasize that Scandinavian bears can be dependent on a single food resource during a critical period of the year and are therefore less resilient to environmental change than expected for an omnivore. Future climate scenarios predict ambiguous trends for weather covariates that affected crucial stages of berry phenology, preventing a clear prognosis of how climate change may affect long‐term bilberry production.     

Structural equation models suggest that bottom‐up processes override top‐down processes in boreal pikeperch (Sander lucioperca) lakes

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Top‐down and bottom‐up control of periphyton by benthivorous fish and light supply in two streams

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Host–parasitoid persistence over variable spatio‐temporally susceptible habitats: bottom–up effects of ephemeral resources

We experimentally and theoretically investigated the persistence of hosts and parasitoids interacting in a metapopulation structure consisting of ephemeral local patches (MELPs). We used a host–parasitoid system consisting of necrophagous Diptera species and their pupal parasitoids. The basal resources used by the host species were assumed to be ephemeral, supporting only one generation of individuals before completely disappearing from the environment. We experimentally measured the host–parasitoid persistence and the effects of local demographic processes in two scenarios: 1) constant occurrence of basal resources at a single site (no dispersion or colonization of other sites) and 2) variable occurrence of basal resources between two sites (colonization of a new patch requiring species dispersal). The experimental setup and findings were then formalized into a mathematical model describing the interaction dynamics in a MELP structure. We evaluated the contribution of several factors to the host–parasitoid coexistence, such as resource allocation probability (probability of resource appearance in a site), variation in resource size and number of sites available to receive resources in the MELP. We found that demographic fluctuations and environmental stochasticity affected the density of migrants, patch habitat connectivity, persistence and spatial distribution of interacting species.     

Temperature indirectly affects benthic microalgal diversity by altering effects of top–down but not bottom–up control

Understanding the ecological mechanisms that underlie species diversity decline in response to environmental change has become an urgent objective in current ecological research. Not only direct (lethal) effects on single species but also indirect effects altering biotic interactions between species within and across trophic levels comprise the driving force of ecosystem change. In an experimental marine benthic microalgae–grazer system we tested for indirect effects of moderate temperature change on algal diversity by manipulation of temperature, nutrient supply and grazer density. In our model system warming did not exert indirect effects on microalgal diversity via effects on resource competition. However, moderate warming strengthened consumer control and thereby indirectly affected algal community structure which ultimately resulted in decreased diversity. Only in low temperature and low nutrient regimes did the antagonizing mechanisms of bottom–up and top–down regulation establish a balancing effect on algal diversity within 29 days (corresponding to 15–29 algae generations). Effects of thermal habitat change did not appear before 9–18 algae generations, which points to the relevance of longer‐term experiments and ecological monitoring in order to separate transient biotic responses and subtle changes of community dynamics in consequence to global change.     

Seasonal,inter‐annual and long term variation in top–down versus bottom–up regulation of primary production

Environmental change strongly affects primary productivity of ecosystems via modifying bottom–up and top–down regulation of primary producers. Here we present a novel approach to quantify the relative importance of regulating factors in natural systems over various time scales: we calculated daily effect sizes of major factors affecting phytoplankton growth during the spring bloom period during almost three decades of lake oligotrophication using numerical experiments with a data based simulation model. We show that with oligotrophication the regulation of spring phytoplankton shifts from primarily top–down to bottom–up, and that the changes in regulation are non‐linearly related to the nutrient (phosphorus) concentrations. Our findings indicate that long‐term changes in top–down regulation cannot be understood without considering multiple herbivore taxa, here, microzooplankton (ciliates) and mesozooplankton (daphnids). We further demonstrate that bottom–up and top–down regulation are not independent from each other and that their interaction is time‐scale dependent.     

How to measure top–down vs bottom–up effects: a new population metric and its calibration on Daphnia

Research on the role of top–down (predation) and bottom–up (food) effects in food webs has led to the understanding that the variability of these effects in space and time is a fundamental feature of natural systems. Consequently, our measurement tools must allow us to evaluate the effects from a dynamical perspective. A population‐dynamics approach may be appropriate to the task. More specifically, because food and predators both affect birth rate, birth rate dynamics may be a key to understanding their impact on the population of interest. Based on the Edmondson–Paloheimo model for birth rate, we propose a new population metric to assess the relative strength of top–down vs bottom–up effects. The metric is the ratio of contributions of changes in proportion of adults and fecundity to change in birth rate. Proportion of adults reflects a top–down effect (predators are assumed to be size‐selective), fecundity reflects a bottom–up effect, and birth rate appears as a common currency with which to compare the former and the latter. Using microcosm experiments and computer simulations on the cladoceran Daphnia, we calibrate the metric and show that, in both types of tests, the ratio of contributions is typically 0.5–0.7 under a strong bottom–up effect and 2.0–2.2 under a strong top–down effect. This provides experimental evidence that the ratio of contributions may allow one to distinguish a strong top–down effect from a strong bottom–up effect.     

The paradox of re‐oligotrophication: the role of bottom–up versus top–down controls on the phytoplankton community

Increases in phytoplankton biomass have been widely observed over the past decades, even in lakes experiencing nutrient reduction. However, the mechanisms giving rise to this trend remain unclear. Here, we unveil the potential mechanisms through quantifying the relative contribution of bottom–up versus top–down control in determining biomasses of phytoplankton assemblages in Lake Geneva. Specifically, we apply nonlinear time series analysis, convergent cross mapping (CCM), to decipher the degree of bottom–up versus top–down control among phytoplankton assemblages via quantifying 1) causal links between environmental factors and various phytoplankton assemblages and 2) the relative importance of bottom–up, top–down, and environmental effects. We show that the recent increase in total phytoplankton biomass, albeit with phosphorus reduction, was mainly caused by a particular phytoplankton assemblage which was better adapted to the re‐oligotrophicated environment characterized by relatively low phosphorus concentrations and warm water temperature, and poorly controlled by zooplankton grazing. Our findings suggest that zooplankton act as a critical driver of phytoplankton biomass and strongly impact the dynamics of recovery from eutrophication. Therefore, our phytoplankton assemblage approach in combination with causal identification of top–down versus bottom–up controls provides insights into the reason why phytoplankton biomass may increase in lakes undergoing phosphorus reduction.     

Pitfalls in histone propionylation during bottom‐up mass spectrometry analysis

Despite their important role in regulating gene expression, posttranslational histone modifications remain technically challenging to analyze. For identification by bottom‐up MS, propionylation is required prior to and following trypsin digestion. Hereby, more hydrophobic peptides are generated enabling RP HPLC separation. When histone dynamics are studied in a quantitative manner, specificity, and efficiency of this chemical derivatization are crucial. Therefore we examined eight different protocols, including two different propionylation reagents. This revealed amidation (up to 70%) and methylation (up to 9%) of carboxyl groups as a side reaction. Moreover, incomplete (up to 85%) as well as a specific propionylation (up to 63%) can occur, depending on the protocol. These results highlight the possible pitfalls and implications for data analysis when doing bottom‐up MS on histones.     

Recent land‐use changes affect stream ecosystem processes in a subtropical island in Brazil

Land‐use changes such as conversion of natural forest to rural and urban areas have been considered as main drivers of ecosystem functions decline, and a large variety of indicators has been used to investigate these effects. Here, we used a replicated litter‐bag experiment to investigate the effects of land‐use changes on the leaf‐litter breakdown process and leaf‐associated invertebrates along the forest–pasture–urban gradient located in a subtropical island (Florianópolis, SC, Brazil). We identified the invertebrates and measured the litter breakdown rates using the litter bags approach. Litter bags containing 3 g of dry leaf of Alchornea triplinervia were deployed on forest rural and urban streams. Principal component analysis, based on physico‐chemical variables which, confirmed a gradient of degradation from forest to urban streams with intermediate values in rural areas. In accordance, shredder richness and abundance were lower in rural and urban than in forest streams. The land‐use changes led also to the dominance of tolerant generalist taxa (Chironomidae and Oligochaeta) reducing the taxonomic and functional diversity in these sites. Leaf‐litter breakdown rates decreased from forest to rural and finally to urban areas and were associated with changes in pH, water velocity, dissolved oxygen and abundance of leaf‐shredding invertebrates, although global decomposition rates did not differ between rural and urban streams. Overall, this study showed that land‐use changes, namely to rural and urban areas, have a strong impact on tropical streams ecosystems, in both processes and communities composition and structure. Despite of being apparently a smaller transformation of landscape, rural land use is comparable to urbanisation in terms of impact in stream functioning. It is thus critical to carefully plan urban development and maintain forest areas in the island of Florianópolis in order to preserve its natural biodiversity and aquatic ecosystems functioning.     

Density‐ and trait‐mediated top–down effects modify bottom–up control of a highly endemic tropical aquatic food web

Benthic invertebrates mediate bottom–up and top–down influences in aquatic food webs, and changes in the abundance or traits of invertebrates can alter the strength of top–down effects. Studies assessing the role of invertebrate abundance and behavior as controls on food web structure are rare at the whole ecosystem scale. Here we use a comparative approach to investigate bottom–up and top–down influences on whole anchialine pond ecosystems in coastal Hawai‘i. In these ponds, a single species of endemic atyid shrimp (Halocaridina rubra) is believed to structure epilithon communities. Many Hawaiian anchialine ponds and their endemic fauna, however, have been greatly altered by bottom–up (increased nutrient enrichment) and top–down (introduced fish predators) disturbances from human development. We present the results of a survey of dissolved nutrient concentrations, epilithon biomass and composition, and H. rubra abundance and behavior in anchialine ponds with and without invasive predatory fish along a nutrient concentration gradient on the North Kona coast of Hawai‘i. We use linear models to assess 1) the effects of nutrient loading and fish introductions on pond food web structure and 2) the role of shrimp density and behavior in effecting that change. We find evidence for bottom–up food web control, in that nutrients were associated with increased epilithon biomass, autotrophy and nutrient content as well as increased abundance and size of H. rubra. We also find evidence for top–down control, as ponds with invasive predatory fish had higher epilithon biomass, productivity, and nutrient content. Top–down effects were transmitted by both altered H. rubra abundance, which changed the biomass of epilithon, and H. rubra behavior, which changed the composition of the epilithon. Our study extends experimental findings on bottom–up and top–down control to the whole ecosystem scale and finds evidence for qualitatively different effects of trait‐ and density‐mediated change in top–down influences.     

Top‐down and bottom‐up control of litter decomposers in streams

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