Assessing top-down and bottom-up control in a litter-based soil macroinvertebrate food chain

The relative importance of top-down and bottom-up control in setting the equilibrium abundances within trophic levels is examined in a comparative study on the litter-based food chain of a temperate deciduous forest. During two consecutive years, we estimated the abundances of macroinvertebrate detritivores and their predators on a natural gradient of annual litterfall. Detritus-based food chains are thought to be classical examples of donor-controlled systems. Indeed, both trophic levels showed higher abundances on sites with higher annual litterfall. Therefore, they appear to be bottom-up controlled. Using the Errors-in-Variables regression technique, we quantitatively compared our data with the equilibrium predictions of a set of simple trophic chain models including bottom-up effects with different types of functional responses (Beddington-DeAngelis, Hassell-Varley, and ratio-dependent). The model with a Hassell-Varley type functional response yielded the best adjustment to the data, although with a very high value of the mutual interference parameter suggesting the existence of overcompensating density dependence. Several changes to the structure of this model were considered. Their adjustment to the data consistently yielded such high values of the interference parameter.     

Complex numerical responses to top-down and bottom-up processes in vertebrate populations

Population growth rate is determined in all vertebrate populations by food supplies, and we postulate bottom-up control as the universal primary standard. But this primary control system can be overridden by three secondary controls: top-down processes from predators, social interactions within the species and disturbances. Different combinations of these processes affect population growth rates in different ways. Thus, some relationships between growth rate and density can be hyperbolic or even have multiple nodes. We illustrate some of these in marsupial, ungulate and rabbit populations. Complex interactions between food, predators, environmental disturbance and social behaviour produce the myriad observations of population growth in nature, and we need to develop generalizations to classify populations. Different animal groups differ in the combination of these four processes that affect them, in their growth rates and in their vulnerability to extinction. Because conservation and management of populations depend critically on what factors drive population growth, we need to develop universal generalizations that will relieve us from the need to study every single population before we can make recommendations for management.     

Climate-induced changes in bottom-up and top-down processes independently alter a marine ecosystem

Climate change has complex structural impacts on coastal ecosystems. Global warming is linked to a widespread decline in body size, whereas increased flood frequency can amplify nutrient enrichment through enhanced run-off. Altered population body-size structure represents a disruption in top-down control, whereas eutrophication embodies a change in bottom-up forcing. These processes are typically studied in isolation and little is known about their potential interactive effects. Here, we present the results of an in situ experiment examining the combined effects of top-down and bottom-up forces on the structure of a coastal marine community. Reduced average body mass of the top predator (the shore crab, Carcinus maenas) and nutrient enrichment combined additively to alter mean community body mass. Nutrient enrichment increased species richness and overall density of organisms. Reduced top-predator body mass increased community biomass. Additionally, we found evidence for an allometrically induced trophic cascade. Here, the reduction in top-predator body mass enabled greater biomass of intermediate fish predators within the mesocosms. This, in turn, suppressed key micrograzers, which led to an overall increase in microalgal biomass. This response highlights the possibility for climate-induced trophic cascades, driven by altered size structure of populations, rather than species extinction.     

Seasonal variation in top-down and bottom-up processes in a grassland arthropod community

Both top-down and bottom-up processes are common in terrestrial ecosystems, but how these opposing forces interact and vary over time is poorly understood. We tested the variation of these processes over seasonal time in a natural temperate zone grassland, a field site characterized by strong seasonal changes in abiotic and biotic conditions. Separate factorial experiments manipulating nutrients and cursorial spiders were performed in the wet and dry seasons. We also performed a water-addition experiment during the summer (dry season) to determine the degree of water limitation during this time. In the spring, nutrient addition increased plant growth and carnivore abundance, indicating a bottom-up control process. Among herbivores, sap-feeders were significantly enhanced while grazers significantly declined resulting in no net change in herbivore abundance. In the summer, water limitation was predominant increasing plants and all herbivores while nutrient (N) effects were non-significant. Top-down processes were present only in the spring season and only impacted the guild of grazing herbivores. These results show that bottom-up limitation is present throughout the season in this grassland, although the specific limiting resource changes as the season progresses. Bottom-up processes affected all trophic levels and many different guilds, while top-down effects were limited to a select group of herbivores and did not extend to the plant trophic level. Our results show that the relative strengths of top-down and bottom-up processes can shift over relatively short periods of time in habitats with a strong seasonal component.     

Warming shifts top-down and bottom-up control of pond food web structure and function

The effects of global and local environmental changes are transmitted through networks of interacting organisms to shape the structure of communities and the dynamics of ecosystems. We tested the impact of elevated temperature on the top-down and bottom-up forces structuring experimental freshwater pond food webs in western Canada over 16 months. Experimental warming was crossed with treatments manipulating the presence of planktivorous fish and eutrophication through enhanced nutrient supply. We found that higher temperatures produced top-heavy food webs with lower biomass of benthic and pelagic producers, equivalent biomass of zooplankton, zoobenthos and pelagic bacteria, and more pelagic viruses. Eutrophication increased the biomass of all organisms studied, while fish had cascading positive effects on periphyton, phytoplankton and bacteria, and reduced biomass of invertebrates. Surprisingly, virus biomass was reduced in the presence of fish, suggesting the possibility for complex mechanisms of top-down control of the lytic cycle. Warming reduced the effects of eutrophication on periphyton, and magnified the already strong effects of fish on phytoplankton and bacteria. Warming, fish and nutrients all increased whole-system rates of net production despite their distinct impacts on the distribution of biomass between producers and consumers, plankton and benthos, and microbes and macrobes. Our results indicate that warming exerts a host of indirect effects on aquatic food webs mediated through shifts in the magnitudes of top-down and bottom-up forcing.     

On the different nature of top-down and bottom-up effects in pelagic food webs

SUMMARY 1. Each individual planktonic plant or animal is exposed to the hazards of starvation and risk of predation, and each planktonic population is under the control of resource limitation from the bottom up (growth and reproduction) and by predation from the top down (mortality). While the bottom-up and top-down impacts are traditionally conceived as compatible with each other, field population-density data on two coexisting Daphnia species suggest that the nature of the two impacts is different. Rates of change, such as the rate of individual body growth, rate of reproduction, and each species' population growth rate, are controlled from the bottom up. State variables, such as biomass, individual body size and population density, are controlled from the top down and are fixed at a specific level regardless of the rate at which they are produced.
2. According to the theory of functional responses, carnivorous and herbivorous predators react to prey density rather than to the rate at which prey are produced or reproduced. The predator's feeding rate (and thus the magnitude of its effect on prey density) should hence be regarded as a functional response to increasing resource concentration.
3. The disparity between the bottom-up and top-down effects is also apparent in individual decision making, where a choice must be made between accepting the hazards of hunger and the risks of predation (lost calories versus loss of life).
4. As long as top-down forces are effective, the disparity with bottom-up effects seems evident. In the absence of predation, however, all efforts of an individual become subordinate to the competition for resources. Biomass becomes limited from the bottom up as soon as the density of a superior competitor has increased to the carrying capacity of a given habitat. Such a shift in the importance of bottom-up control can be seen in zooplankton in habitats from which fish have been excluded.     

Integral membrane proteins: bottom-up,top-down and structural proteomics

Introduction: Integral membrane proteins and lipids constitute the bilayer membranes that surround cells and sub-cellular compartments, and modulate movements of molecules and information between them. Since membrane protein drug targets represent a disproportionately large segment of the proteome, technical developments need timely review.

Areas covered: Publically available resources such as Pubmed were surveyed. Bottom-up proteomics analyses now allow efficient extraction and digestion such that membrane protein coverage is essentially complete, making up around one third of the proteome. However, this coverage relies upon hydrophilic loop regions while transmembrane domains are generally poorly covered in peptide-based strategies. Top-down mass spectrometry where the intact membrane protein is fragmented in the gas phase gives good coverage in transmembrane regions, and membrane fractions are yielding to high-throughput top-down proteomics. Exciting progress in native mass spectrometry of membrane protein complexes is providing insights into subunit stoichiometry and lipid binding, and cross-linking strategies are contributing critical in-vivo information.

Expert commentary: It is clear from the literature that integral membrane proteins have yielded to advanced techniques in protein chemistry and mass spectrometry, with applications limited only by the imagination of investigators. Key advances toward translation to the clinic are emphasized.     

Adaptive genetic variation mediates bottom-up and top-down control in an aquatic ecosystem

Research in eco-evolutionary dynamics and community genetics has demonstrated that variation within a species can have strong impacts on associated communities and ecosystem processes. Yet, these studies have centred around individual focal species and at single trophic levels, ignoring the role of phenotypic variation in multiple taxa within an ecosystem. Given the ubiquitous nature of local adaptation, and thus intraspecific variation, we sought to understand how combinations of intraspecific variation in multiple species within an ecosystem impacts its ecology. Using two species that co-occur and demonstrate adaptation to their natal environments, black cottonwood (Populus trichocarpa) and three-spined stickleback (Gasterosteus aculeatus), we investigated the effects of intraspecific phenotypic variation on both top-down and bottom-up forces using a large-scale aquatic mesocosm experiment. Black cottonwood genotypes exhibit genetic variation in their productivity and consequently their leaf litter subsidies to the aquatic system, which mediates the strength of top-down effects from stickleback on prey abundances. Abundances of four common invertebrate prey species and available phosphorous, the most critically limiting nutrient in freshwater systems, are dictated by the interaction between genetic variation in cottonwood productivity and stickleback morphology. These interactive effects fit with ecological theory on the relationship between productivity and top-down control and are comparable in strength to the effects of predator addition. Our results illustrate that intraspecific variation, which can evolve rapidly, is an under-appreciated driver of community structure and ecosystem function, demonstrating that a multi-trophic perspective is essential to understanding the role of evolution in structuring ecological patterns.     

Plankton dynamics in a tropical floodplain lake: fish, nutrients, and the relative importance of bottom-up and top-down control

1. Two enclosure experiments were carried out in Laguna Bufeos, a neotropical várzea lake located in the floodplain of River Ichilo (Bolivia). The experiments aimed (i) to assess the relative importance of bottom‐up and top‐down control on the plankton community, (ii) to assess the relative impact of direct and indirect effects of planktivorous fish on the zooplankton, and (iii) to attempt to identify the mechanisms responsible for these effects. 2. During the first experiment, bottom‐up control seemed to dominate the planktonic food web. Compared with fishless enclosures, oxygen concentrations, chlorophyll a levels and the population densities of all cladoceran zooplankton taxa increased in enclosures with fish. Birth rates of Moina minuta, the dominant taxon, were substantially higher in the presence than in the absence of fish, whereas death rates did not differ between treatments. These results are the first to suggest that the positive effects of fish on crustacean zooplankton via effects on nutrient cycling and the enhancement of primary production can compensate for losses because of fish‐related mortality. 3. During the second experiment, the direction of control appeared to vary between trophic levels: the phytoplankton appeared to be bottom‐up controlled whereas the zooplankton was mainly top‐down controlled. Chlorophyll a concentrations were enhanced by both fish and nutrient additions. The majority of the zooplankton taxa were reduced by the presence of fish. Birth rates of most cladoceran taxa did not differ between treatments, whereas death rates were higher in the enclosures with fish than in the fishless enclosures. Bosminopsis deitersi reached higher densities in the presence of fish, probably because of a release from predation by Chaoborus. 4. We convincingly showed strong deviations from trophic cascade‐based expectations, supporting the idea that trophic cascades may be weak in tropical lakes.     

From plankton to top predators: bottom-up control of a marine food web across four trophic levels

1. Abundant mid-trophic pelagic fish often play a central role in marine ecosystems, both as links between zooplankton and top predators and as important fishery targets. In the North Sea, the lesser sandeel occupies this position, being the main prey of many bird, mammal and fish predators and the target of a major industrial fishery. However, since 2003, sandeel landings have decreased by > 50%, and many sandeel-dependent seabirds experienced breeding failures in 2004. 2. Despite the major economic implications, current understanding of the regulation of key constituents of this ecosystem is poor. Sandeel abundance may be regulated 'bottom-up' by food abundance, often thought to be under climatic control, or 'top-down' by natural or fishery predation. We tested predictions from these two hypotheses by combining unique long-term data sets (1973-2003) on seabird breeding productivity from the Isle of May, SE Scotland, and plankton and fish larvae from the Continuous Plankton Recorder survey. We also tested whether seabird breeding productivity was more tightly linked to sandeel biomass or quality (size) of individual fish. 3. The biomass of larval sandeels increased two- to threefold over the study period and was positively associated with proxies of the abundance of their plankton prey. Breeding productivity of four seabirds bringing multiple prey items to their offspring was positively related to sandeel larval biomass with a 1-year lag, indicating dependence on 1-year-old fish, but in one species bringing individual fish it was strongly associated with the size of adult sandeels. 4. These links are consistent with bottom-up ecosystem regulation and, with evidence from previous studies, indicate how climate-driven changes in plankton communities can affect top predators and potentially human fisheries through the dynamics of key mid-trophic fish. However, the failing recruitment to adult sandeel stocks and the exceptionally low seabird breeding productivity in 2004 were not associated with low sandeel larval biomass in 2003, so other mechanisms (e.g. predation, lack of suitable food after metamorphosis) must have been important in this case. Understanding ecosystem regulation is extremely important for predicting the fate of keystone species, such as sandeels, and their predators.     

Bottom-up rather than top-down processes regulate the abundance and activity of nitrogen fixing plants in two Connecticut old-field ecosystems

The maintenance of nitrogen limitation in terrestrial ecosystems remains a central paradox in biogeochemistry. Although plants that form a symbiotic association with nitrogen fixing bacteria should be at a competitive advantage over non-fixing plant species in N limited environments, N₂ fixing plants are uncommon in most mid- to high-latitude ecosystems. Theory and observation suggest that preferential grazing on N-rich tissues by herbivores, resource limitations to growth, reproduction and N₂ fixation, and temperature limitations to the activity of the N₂ fixing enzyme nitrogenase, explain the rarity of N₂ fixing plants. These ideas, however, have never been confronted by multifactor experiments in the field. In a 3 year field experiment, we found that the abundance, growth, reproductive output and fraction of plant-N derived from N₂ fixation in temperate, old-field ecosystems was constrained by the availability of phosphorus (P). Although the availability of light was crucial to the performance of old-field N₂ fixing plants, the largest gains in biomass and the rate of N₂ fixation were observed in the plots fertilized with P. By contrast, herbivory had no effect on the abundance, biomass and activity of N₂ fixing plants and inconsistent effects on foliar nitrogen concentrations (opposing directions, depending upon year), suggesting that herbivores do not affect the ecology of N₂ fixing plants in old field ecosystems, at least not over the course of 3 years. Together with a recent study demonstrating that C limitation explains the absence of N₂ fixing trees in temperate forests our analysis suggests that stand replacing disturbances shift the limitation on the abundance and activity of N₂ fixing plants from P early in secondary succession to light later in succession, as the forest canopy closes and incident light levels decline precipitously.     

Comparing effectiveness of top-down and bottom-up strategies in containing influenza

This research compares the performance of bottom-up, self-motivated behavioral interventions with top-down interventions targeted at controlling an "Influenza-like-illness". Both types of interventions use a variant of the ring strategy. In the first case, when the fraction of a person's direct contacts who are diagnosed exceeds a threshold, that person decides to seek prophylaxis, e.g. vaccine or antivirals; in the second case, we consider two intervention protocols, denoted Block and School: when a fraction of people who are diagnosed in a Census Block (resp., School) exceeds the threshold, prophylax the entire Block (resp., School). Results show that the bottom-up strategy outperforms the top-down strategies under our parameter settings. Even in situations where the Block strategy reduces the overall attack rate well, it incurs a much higher cost. These findings lend credence to the notion that if people used antivirals effectively, making them available quickly on demand to private citizens could be a very effective way to control an outbreak.     

The dynamics of top-down and bottom-up effects in food webs of varying prey diversity, composition, and productivity

Prey diversity is thought to mediate the strength of top-down and bottom-up effects, but few experiments directly test this hypothesis. I assembled food webs of bacteria and bacterivorous protist prey in laboratory microcosms with all combinations of five productivity levels, two top predator treatments (present or absent), and three prey compositions. Depauperate food chains contained one of two edible prey species, while more diverse food webs contained both edible prey species plus two additional less-edible/inedible prey. Equilibrium theory predicts that prey diversity should weaken the top-down and bottom-up effects on trophic level biomasses, due to density compensation among prey species. Top-down effects should increase with productivity in food chains, but decrease with productivity in food webs. Results revealed highly dynamic top-down effects, the strength of which varied more over time than among treatments. Further, top-down effects did not merely vary in absolute strength over time, but also in relative strength across different prey compositions and productivity levels. It might be expected that equilibrium models would qualitatively reproduce time-averaged results. However, time-averaged data largely failed to support equilibrium predictions. This failure may reflect strong temporal variability in treatment effects combined with nonlinear density dependence of species' per-capita growth rates. Strong temporal variability in the strength of top-down effects has not previously been demonstrated, but likely is common in nature as well.     

Bottom-up and top-down processes interact to modify intraguild interactions in resource-pulse environments

Top predators are declining globally, in turn allowing populations of smaller predators, or mesopredators, to increase and potentially have negative effects on biodiversity. However, detection of interactions among sympatric predators can be complicated by fluctuations in the background availability of resources in the environment, which may modify both the numbers of predators and the strengths of their interactions. Here, we first present a conceptual framework that predicts how top-down and bottom-up interactions may regulate sympatric predator populations in environments that experience resource pulses. We then test it using 2 years of remote-camera trapping data to uncover spatial and temporal interactions between a top predator, the dingo Canis dingo, and the mesopredatory European red fox Vulpes vulpes and feral cat Felis catus, during population booms, declines and busts in numbers of their prey in a model desert system. We found that dingoes predictably suppress abundances of the mesopredators and that the effects are strongest during declines and busts in prey numbers. Given that resource pulses are usually driven by large yet infrequent rains, we conclude that top predators like the dingo provide net benefits to prey populations by suppressing mesopredators during prolonged bust periods when prey populations are low and potentially vulnerable.     

Crop domestication relaxes both top-down and bottom-up effects on a specialist herbivore

Domestication of crop plants selects for numerous traits that often distinguish them dramatically from their wild progenitors. In some cases, these modifications lead to increased herbivory, by enhancing their attractiveness to herbivorous insects or reducing the efficiency of natural enemies, or both. This study investigated the effects of fruit enlargement on the olive (Olea europaea L.), the specialist olive fruit fly, Bactrocera oleae (Rossi), and its specialized larval parasitoids. Wild olive fruit are small (<2 mm pulp thickness) and the larval parasitoids associated with B. oleae have short ovipositors (<3 mm), while cultivated fruit are larger (4–8 mm pulp thickness). Female flies allocate more offspring to large than to small fruit within or across different-sized commercial cultivars, without reducing the fitness of their offspring. Fly larvae move deeper into the olive pulp with their increasing age and fruit size. In contrast, the specialist larval parasitoid, Psyttalia lounsburyi (Silvestri), more effectively parasitizes hosts in smaller than larger fruit. The inverse relationship between the performance of the fly and its co-evolved parasitoids on fruit of increasing sizes indicates that olive cultivation favors the success of the fly by providing a better food resource and more enemy-free space. These findings offer some explanation for the failure of the decades-old classical biological efforts to manage B. oleae using specialized larval parasitoids in the Mediterranean Basin and provide further evidence that crop domestication can alter host–parasitoid interactions.     

Effects of bottom-up and top-down controls on the temporal distribution of planktonic heterotrophic nanoflagellates are dependent on water depth

The ecological function of the Mesopotamian marshlands was severely damaged during their desiccation from 1993 to 2003 and, as a result, the marshes became a main target for restoration after their re-flooding in April 2003. In this study, the phosphorus (P) and nitrogen (N) budgets for a portion of the Mesopotamian marshlands at Al-Hawizeh (Iraq) are reported. Al-Hawizeh appears to play a strong role in regulating P and N. Total P input and output were both dominated by dissolved organic P, while total N input and output were dominated by particulate organic N, suggesting that N is in greater demand than P. Al-Hawizeh acts as source for N and sink for P; this has an important function in altering their export downstream (Shatt Al-Arab River) and subsequently into the Arabian Gulf. However, investigating P and N fractions helped in understanding the role of Al-Hawizeh in transforming, storage and release of P and N fractions.     

Comparative and experimental approaches to top-down and bottom-up regulation of bacteria

The regulation of bacterial community biomass and productivity by resources and predators is a central concern in the study of microbial food webs. Resource or bottom-up regulation refers to the limitation of bacteria by carbon and nutrients derived from allocthonous inputs, primary production, and heterotrophic production. Predatory or top-down regulation refers to the limitation of bacteria below levels supportable by resources alone. Large scale comparative studies demonstrate strong correlations between bacterial productivity and biomass, suggesting significant resource regulation. Comparisons of the abundances of heterotrophic flagellates and bacteria, however, imply that in some cases there may be top-down regulation of bacteria in eutrophic environments. Experimental studies in lakes support the importance of resource regulation and reveal little top-down control from protozoans. Increases in bacterial abundance and production with nutrient enrichment were limited in enclosure experiments with high abundances of the cladoceran, Daphnia. Regulation of bacteria by Daphnia may occur in many lakes seasonally and prevail in some lakes throughout the year where these animals sustain dense populations. In most situations, however, bacteria appear to be limited primarily by resources.     

Intraguild interactions between spiders and ants and top-down control in a grassland food web

In most terrestrial ecosystems ants (Formicidae) as eusocial insects and spiders (Araneida) as solitary trappers and hunters are key predators. To study the role of predation by these generalist predators in a dry grassland, we manipulated densities of ants and spiders (natural and low density) in a two-factorial field experiment using fenced plots. The experiment revealed strong intraguild interactions between ants and spiders. Higher densities of ants negatively affected the abundance and biomass of web-building spiders. The density of Linyphiidae was threefold higher in plots without ant colonies. The abundance of Formica cunicularia workers was significantly higher in spider-removal plots. Also, population size of springtails (Collembola) was negatively affected by the presence of wandering spiders. Ants reduced the density of Lepidoptera larvae. In contrast, the abundance of coccids (Ortheziidae) was positively correlated with densities of ants. To gain a better understanding of the position of spiders, ants and other dominant invertebrate groups in the studied food web and important trophic links, we used a stable isotope analysis (¹⁵N and ¹³C). Adult wandering spiders were more enriched in ¹⁵N relative to ¹⁴N than juveniles, indicating a shift to predatory prey groups. Juvenile wandering and web-building spiders showed δ¹⁵N ratios just one trophic level above those of Collembola, and they had similar δ¹³C values, indicating that Collembola are an important prey group for ground living spiders. The effects of spiders demonstrated in the field experiment support this result. We conclude that the food resource of spiders in our study system is largely based on the detrital food web and that their effects on herbivores are weak. The effects of ants are not clear-cut and include predation as well as mutualism with herbivores. Within this diverse predator guild, intraguild interactions are important structuring forces.     

Alternation of bottom-up and top-down regulation in a natural population of an agromyzid leafminer,Chromatomyia suikazurae

The population dynamics and the relative importance of bottom-up and top-down effects in a plant-leafminer-multiparasitoid interaction was studied between 1981 and 1990 in a natural forest in Kyoto, Japan. The leafminer, Chromatomyia suikazurae (Agromyzidae, Diptera), passed two generations (G1 and G2) on Lonicera gracilipes (Caprifoliaceae). The G1 population in February was free from parasitoid attack, and the mortality in G1 was mainly caused by resource limitation. Intraspecific competition for resources occurred at the larval stage in G1, and the larval mortality was density-dependent. The G1 adult density was resource-limited (the number of newly opened leaves), and its variability was lower than that of G2. The G2 population in April was not resource-limited but subject to intense attack by a species-rich parasitoid complex, and thus total mortality was much larger than that in G1. Significant density dependence was detected not in larval but in pupal mortalities, which were mainly caused by parasitism by parasitoids that attacked the pupa. The host population alternately experienced bottom-up effects during the larval stage in G1 and top-down effects during the pupal stage in G2. Overall population fluctuation was non-cyclic and mainly due to climatically-induced fluctuation of available plant resources in G1.