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.     

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.     

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.     

Ecological significance and classification of Chinese wetlands

China supports a great variety of wetlands, including some of the most important in the world. However, an appropriate classification system applicable to all wetlands is not available. Based on a preliminary inventory, a new classification system for Chinese wetlands is proposed. This system classifies natural wetlands into three categories on the basis of their natural features and distribution: peatlands, coastal and estuarine wetlands, and riverine and lacustrine wetlands. Each category is divided into several sub-classes. The areal extent of wetlands in each Province has been estimated and their ecological importance assessed.     

Wedged between bottom-up and top-down processes: aphids on tansy

Abstract. 1. Many species of aphids exploit a single host‐plant species and have to cope with changing environmental conditions. They often vary greatly in abundance even when feeding on the same host. In a field experiment, the bottom‐up (plant quality/patch type frequency) and top‐down (ant attendance/predation) effects on the abundance of four species of aphids feeding on tansy (Tanacetum vulgare) were tested using a full factorial design. In addition, a model was used to examine these patch characteristics for their relative effects on the population dynamics and abundance of different aphid species. 2. Aphid numbers changed significantly depending on the quality of the host plant and the presence/absence of attending ants. The obligate myrmecophile, Metopeurum fuscoviride, was abundant on high‐quality plants, while on poor quality plants or on plants without attending ants these aphids did not survive until the end of the experiment. The facultative myrmecophiles, Aphis fabae and Brachycaudus cardui, and the unattended aphid species, Macrosiphoniella tanacetaria, all reached similar peak population densities, but M. tanacetaria did best in poor quality patches. 3. Natural enemies reduced aphid numbers, but those species feeding on high‐quality plants survived longer than those on poor‐quality plants, which existed only for a short period of time, especially when associated with ants. Losses due to migration of winged morphs and mortality caused by parasitoids were insignificant. 4. Varying the frequency of different patch types in a model indicates that different degrees of associations with ants are favoured in different environments. If the proportion of high‐quality patches in a habitat is large, obligate myrmecophiles do best. On increasing the number of poor‐quality patches, unattended species become more abundant. 5. The results suggest that, in spite of large species specific differences in growth rates, degree of myrmecophily or life cycle features, the temporal and spatial variability in top‐down and bottom‐up forces differentially affects aphid species and allows the simultaneous exploitation of a shared host‐plant species.     

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.     

Positive feedbacks between bottom-up and top-down controls promote the formation and toxicity of ecosystem disruptive algal blooms: A modeling study

Harmful algal blooms that disrupt and degrade ecosystems (ecosystem disruptive algal blooms, EDABs) are occurring with greater frequency and severity with eutrophication and other adverse anthropogenic alterations of coastal systems. EDAB events have been hypothesized to be caused by positive feedback interactions involving differential growth of competing algal species, low grazing mortality rates on EDAB species, and resulting decreases in nutrient inputs from grazer-mediated nutrient cycling as the EDAB event progresses. Here we develop a stoichiometric nutrient–phytoplankton–zooplankton (NPZ) model to test a conceptual positive feedback mechanism linked to increased cell toxicity and resultant decreases in grazing mortality rates in EDAB species under nutrient limitation of growth rate. As our model EDAB alga, we chose the slow-growing, toxic dinoflagellate Karenia brevis, whose toxin levels have been shown to increase with nutrient (nitrogen) limitation of specific growth rate. This species was competed with two high-nutrient adapted, faster-growing diatoms (Thalassiosira pseudonana and Thalassiosira weissflogii) using recently published data for relationships among nutrient (ammonium) concentration, carbon normalized ammonium uptake rates, cellular nitrogen:carbon (N:C) ratios, and specific growth rate. The model results support the proposed positive feedback mechanism for EDAB formation and toxicity. In all cases the toxic bloom was preceded by one or more pre-blooms of fast-growing diatoms, which drew dissolved nutrients to low growth rate-limiting levels, and stimulated the population growth of zooplankton grazers. Low specific grazing rates on the toxic, nutrient-limited EDAB species then promoted the population growth of this species, which further decreased grazing rates, grazing-linked nutrient recycling, nutrient concentrations, and algal specific growth rates. The nutrient limitation of growth rate further increased toxin concentrations in the EDAB algae, which further decreased grazing-linked nutrient recycling rates and nutrient concentrations, and caused an even greater nutrient limitation of growth rate and even higher toxin levels in the EDAB algae. This chain of interactions represented a positive feedback that resulted in the formation of a high-biomass toxic bloom, with low, nutrient-limited specific growth rates and associated high cellular C:N and toxin:C ratios. Together the elevated C:N and toxin:C ratios in the EDAB algae resulted in very high bloom toxicity. The positive feedbacks and resulting bloom formation and toxicity were increased by long water residence times, which increased the relative importance of grazing-linked nutrient recycling to the overall supply of limiting nutrient (N).     

Evidence for differential top-down and bottom-up suppression in posterior parietal cortex

When searching for an object, we usually avoid items that are visually different from the target and objects or places that have been searched already. Previous studies have shown that neural activity in the lateral intraparietal area (LIP) can be used to guide this behaviour; responses to task irrelevant stimuli or to stimuli that have been fixated previously in the trial are reduced compared with responses to potential targets. Here, we test the hypothesis that these reduced responses have a different genesis. Two animals were trained on a visual foraging task, in which they had to find a target among a number of physically identical potential targets (T) and task irrelevant distractors. We recorded neural activity and local field potentials (LFPs) in LIP while the animals performed the task. We found that LFP power was similar for potential targets and distractors but was greater in the alpha and low beta bands when a previously fixated T was in the response field. We interpret these data to suggest that the reduced single-unit response to distractors is a bottom-up feed-forward result of processing in earlier areas and the reduced response to previously fixated Ts is a result of active top-down suppression.     

The annual cycle of heterotrophic freshwater nanoflagellates: role of bottom-up versus top-down control

The population dynamics of heterotrophic nanoflagellates (HNF)were analyzed in pre-alpine Lake Constance over three consecutiveyears. A recurrent seasonal pattern led to the identificationof five seasonal phases: winter, spring, clear-water, summerand autumn. HNF biomass was lowest in winter and highest m latespring several weeks after the phytoplankton spring bloom. Theaverage biomass of HNF was 5–12% of bacterial biomassand 13–34% of ciliate biomass respectively. The largestHNF cells were recorded during the spring phase, whereas theaverage cell size was reduced to one-third during the subsequentclear-water phase. The pronounced differences in the mean cellsize were attributed mainly to varying grazing impact on HNFThroughout most of the year, HNF production was balanced bygrazing of microzooplankton, namely ciliates, within the microbialloop. During the dear-water phase, however, the grazing impactwas mainly due to rotifers and daphnids. Changing grazing impactwas primarily responsible for the observed 2-fold interannualdifference m the mean biomass of HNF Overall, top-down controlby grazing was more important in governing the population dynamicsof HNF than bottom-up control by bacterial food supply.     

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.     

Marine ecosystem services: Linking indicators to their classification

There is a multitude of ecosystem service classifications available within the literature, each with its own advantages and drawbacks. Elements of them have been used to tailor a generic ecosystem service classification for the marine environment and then for a case study site within the North Sea: the Dogger Bank. Indicators for each of the ecosystem services, deemed relevant to the case study site, were identified. Each indicator was then assessed against a set of agreed criteria to ensure its relevance and applicability to environmental management. This paper identifies the need to distinguish between indicators of ecosystem services that are entirely ecological in nature (and largely reveal the potential of an ecosystem to provide ecosystem services), indicators for the ecological processes contributing to the delivery of these services, and indicators of benefits that reveal the realized human use or enjoyment of an ecosystem service. It highlights some of the difficulties faced in selecting meaningful indicators, such as problems of specificity, spatial disconnect and the considerable uncertainty about marine species, habitats and the processes, functions and services they contribute to.     

Ecosystem-level evidence for top-down and bottom-up control of production in a grassland stream system

Ecosystem-wide effects of introduced brown trout (Salmo trutta L.) and native river galaxias (Galaxiaseldoni McDowall) were studied by analysing ecosystem production budgets for two adjacent tributaries of a grassland stream-system in the South Island of New Zealand. One tributary was inhabited by brown trout, the other by river galaxias. No other fish species were present in either stream. The budget for the river galaxias stream indicated little top-down control of invertebrates by fish predation (river galaxias consumed ∼18% of available prey production). A large proportion of annual net primary production was required to support production by invertebrates (invertebrates consumed an average of ∼75% of available primary production), and mean surplus primary production (i.e. not consumed) was not significantly different from zero. Primary and secondary production were presumably mutually limiting in this system (i.e. controlled by simultaneous top-down and bottom-up mechanisms). In contrast, the budget for the brown trout stream indicated extreme top-down control of invertebrate populations by fish predation; essentially all invertebrate production (∼100%) was required to support trout production. Invertebrate production required only a minor portion of annual net primary production (∼21%) and primary production was presumably controlled by mechanisms other than grazing (e.g. sloughing, nutrient limitation). Predatory invertebrates had little quantitative effect on prey populations in either stream. Recent experimental studies of invertebrate behaviour, fish behaviour, and food-web structure in New Zealand streams with physically stable channels indicate that a trophic cascade should be observed in streams inhabited by brown trout, in contrast to those inhabited by native fish. The results reported here provide ecosystem-level evidence supporting this prediction. Received: 10 March 1997 / Accepted: 12 December 1997     

The relative importance of top-down and bottom-up control of phytoplankton in a shallow macrophyte-dominated lake

1. Mechanisms stabilizing the plant-dominated clear-water state were investigated in Little Mere, U.K. Replicated, factorial, mesocosm experiments, carried out in 1995 and 1996, were designed to investigate the relative importance of top-down (zooplankton grazing) and bottom-up (nitrogen-limitation) control in limiting algal growth, and the role of macrophytes in these processes. Treatments included increased salinity (1995) and sticklebacks (1996) to reduce zooplankton numbers, weekly nitrate additions and removal of macrophytes. 2. Contrary to the results of other studies, submerged plants did not reduce nitrate concentrations. Owing to the high stickleback density in the enclosures with fish, macrophytes did not provide a refuge for zooplankton during the experiment. In Little Mere, however, where fish densities are lower, macrophytes probably play a key role in maintaining clear water by providing refuge for pelagic zooplankton and habitat for attached Cladocera. 3. Phytoplankton in Little Mere was not nitrogen- (N) limited during the growing season. Although nitrogen availability sets a maximum potential phytoplankton biomass it was not realized owing to control by zooplankton grazing.     

Artificial humification of lignin architecture: Top-down and bottom-up approaches

Humic substances readily identifiable in the environment are involved in several biotic and abiotic reactions affecting carbon turnover, soil fertility, plant nutrition and stimulation, xenobiotic transformation and microbial respiration. Inspired by natural roles of humic substances, several applications of these substances, including crop stimulants, redox mediators, anti-oxidants, human medicines, environmental remediation and fish feeding, have been developed. The annual market for humic substances has grown rapidly for these reasons and due to eco-conscious features, but there is a limited supply of natural coal-related resources such as lignite and leonardite from which humic substances are extracted in bulk. The structural similarity between humic substances and lignin suggests that lignocellulosic refinery resulting in lignin residues as a by-product could be a potential candidate for a bulk source of humic-like substances, but structural differences between the two polymeric materials indicate that additional transformation procedures allowing lignin architecture to fully mimic commercial humic substances are required. In this review, we introduce the emerging concept of artificial humification of lignin-related materials as a promising strategy for lignin valorization. First, the core structural features of humic substances and the relationship between these features and the physicochemical properties, natural functions and versatile applications of the substances are described. In particular, the mechanism by which humic substances stimulate the growth of plants and hence can improve crop productivity is highlighted. Second, top-down and bottom-up transformation pathways for scalable humification of small lignin-derived phenols, technical lignins and lignin-containing plant residues are described in detail. Finally, future directions are suggested for research and development of artificial lignin humification to achieve alternative ways of producing customized analogues of humic substances.     

A unified treatment of top-down and bottom-up control of reproduction in populations

Generalizations describing how top‐down and bottom‐up processes jointly influence the production of offspring (recruitment) and the number of reproducing adults are lacking. This is a deficiency because (1) it is widely recognized that both top‐down and bottom‐up processes are common in ecosystems; and (2) the relationship between the number of individuals recruiting and number of reproductively active individuals present in that population is of fundamental importance in all branches of ecology. Here we derive a model to consider the joint effects of top‐down and bottom‐up forcing in any ecosystem. In general, during the lifetime of a cohort, bottom‐up effects are likely to limit recruitment over longer periods of time than top‐down effects. Top‐down effects are likely to be most important early in the life history when potential recruits are small in size, and such effects will be more recognizable in small cohorts comprised of slowly growing individuals.     

Relative strengths of top-down and bottom-up forces in a tropical forest community

We tested integrative bottom-up and top-down trophic cascade hypotheses with manipulative experiments in a tropical wet forest, using the ant-plant Piper cenocladum and its associated arthropod community. We examined enhanced nutrients and light along with predator and herbivore exclusions as sources of variation in the relative biomass of plants, their herbivores (via rates of herbivory), and resident predaceous ants. The combined manipulations of secondary consumers, primary consumers, and plant resources allowed us to examine some of the direct and indirect effects on each trophic level and to determine the relative contributions of bottom-up and top-down cascades to the structure of the community. We found that enhanced plant resources (nutrients and light) had direct positive effects on plant biomass. However, we found no evidence of indirect (cascading through the herbivores) effects of plant biomass on predators or top predators. In contrast, ants had indirect effects on plant biomass by decreasing herbivory on the plants. This top-down cascade occurred whether or not plant resources were enriched, conditions which are expected to modify top-down forces. Received: 9 August 1998 / Accepted: 1 December 1998     

Canadian wetlands: Environmental gradients and classification

The Canadian Wetland Classification System is based on manifestations of ecological processes in natural wetland ecosystems. It is hierarchical in structure and designed to allow identification at the broadest levels (class, form, type) by non-experts in different disciplines. The various levels are based on broad physiognomy and hydrology (classes); surface morphology (forms); and vegetation physiognomy (types). For more detailed studies, appropriate characterization and subdivisions can be applied. For ecological studies the wetlands can be further characterized by their chemical environment, each with distinctive indicator species, acidity, alkalinity, and base cation content. For peatlands, both chemical and vegetational differences indicate that the primary division should be acidic, Sphagnum-dominated bogs and poor fens on one hand and circumneutral to alkaline, brown moss-dominated rich fens on the other. Non peat-forming wetlands (marshes, swamps) lack the well developed bryophyte ground layer of the fens and bogs, and are subject to severe seasonal water level fluctuations. The Canadian Wetland Classification System has been successfully used in Arctic, Subarctic, Boreal and Temperate regions of Canada.