The Good,the Bad,and the Tiny: A Simple,Mechanistic-Probabilistic Model of Virus-Nutrient Colimitation in Microbes

For phytoplankton and other microbes, nutrient receptors are often the passages through which viruses invade. This presents a bottom-up vs. top-down, co-limitation scenario; how do these would-be-hosts balance minimizing viral susceptibility with maximizing uptake of limiting nutrient(s)? This question has been addressed in the biological literature on evolutionary timescales for populations, but a shorter timescale, mechanistic perspective is lacking, and marine viral literature suggests the strong influence of additional factors, e.g. host size; while the literature on both nutrient uptake and host-virus interactions is expansive, their intersection, of ubiquitous relevance to marine environments, is understudied. I present a simple, mechanistic model from first principles to analyze the effect of this co-limitation scenario on individual growth, which suggests that in environments with high risk of viral invasion or spatial/temporal heterogeneity, an individual host’s growth rate may be optimized with respect to receptor coverage, producing top-down selective pressure on short timescales. The model has general applicability, is suggestive of hypotheses for empirical exploration, and can be extended to theoretical studies of more complex behaviors and systems.     

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.     

Bottom-up and top-down effects in a pre-dispersal seed predation system: are non-predated seeds damaged?

Seed predators that severely affect seed germination rates are well known for many plant species. Here, we hypothesised that due to differences in resource allocation within fruits, seed predation can negatively affect non-predated seeds in infested fruits when predation occurs during fruit maturation (a ‘top-down’ effect). We addressed this question using a system of bruchid beetles on Mimosa trees and we also investigated whether seed quality (nitrogen concentration) affects beetle body mass, which would have implications for adult fitness (‘bottom-up’ effect). To assess spatial variation, bottom-up and top-down effects were investigated in two plant populations. Nitrogen concentration was significantly higher in seeds from non-infested fruits than from infested fruits. This supports the hypothesis that resource allocation may differ between seeds from infested and non-infested fruits. Germination experiments showed that seeds from non-infested fruits germinated better than non-predated seeds from infested fruits. It was also confirmed that seed quality affected bruchid body mass. There was also evidence that more resources were taken from well-developed seeds. These results showed that seed predation can damage non-predated seeds.     

The effect of the Holling type II functional response on apparent competition

This article analyzes the classical 2-resource-1-consumer apparent competition community module with the Holling type II functional response. Two types of resource regulation (top-down vs. combined top-down and bottom-up) and two types of consumer behaviors (inflexible consumers with fixed preferences for resources vs. adaptive consumers) are considered. When resources grow exponentially and consumers are inflexible foragers, one resource is always outcompeted due to strong apparent competition. Density dependent resource growth relaxes apparent competition so that resources can coexist. As multiple attractors (either equilibria or limit cycles) coexist, population dynamics and community composition depend on initial population densities. Population dynamics change dramatically when consumers forage adaptively. In this case, the results both for top-down, and combined top-down and bottom-up regulation are similar and they show that species persistence occurs for a much larger set of parameter values when compared with inflexible consumers. Moreover, population dynamics will be chaotic when resource carrying capacities are high enough. This shows that adaptive consumer switching can destabilize population dynamics.     

Evolved physiological responses of phytoplankton to their integrated growth environment

Phytoplankton growth and productivity relies on light, multiple nutrients and temperature. These combined factors constitute the 'integrated growth environment'. Since their emergence in the Archaean ocean, phytoplankton have experienced dramatic shifts in their integrated growth environment and, in response, evolved diverse mechanisms to maximize growth by optimizing the allocation of photosynthetic resources (ATP and NADPH) among all cellular processes. Consequently, co-limitation has become an omnipresent condition in the global ocean. Here we focus on evolved phytoplankton populations of the contemporary ocean and the varied energetic pathways they employ to solve the optimization problem of resource supply and demand. Central to this discussion is the allocation of reductant formed through photosynthesis, which we propose has the following three primary fates: carbon fixation, direct use and ATP generation. Investment of reductant among these three sinks is tied to cell cycle events, differentially influenced by specific forms of nutrient stress, and a strong determinant of relationships between light-harvesting (pigment), photosynthetic electron transport and carbon fixation. Global implications of optimization are illustrated by deconvolving trends in the 10-year global satellite chlorophyll record into contributions from biomass and physiology, thereby providing a unique perspective on the dynamic nature of surface phytoplankton populations and their link to climate.     

Phytoplankton competition in deep biomass maximum

Resource competition in heterogeneous environments is still an unresolved problem of theoretical ecology. In this article, I analyze competition between two phytoplankton species in a deep water column, where the distributions of main resources (light and a limiting nutrient) have opposing gradients and co-limitation by both resources causes a deep biomass maximum. Assuming that the species have a trade-off in resource requirements and the water column is weakly mixed, I apply the invasion threshold analysis (Ryabov and Blasius, Ecol Lett 14:220–228, 2011) to determine relations between environmental conditions and phytoplankton composition. Although species deplete resources in the interior of the water column, the resource levels at the bottom and surface remain high. As a result, the slope of resources gradients becomes a new crucial factor which, rather than the local resource values, determines the outcome of competition. The value of resource gradients nonlinearly depend on the density of consumers. This leads to complex relationships between environmental parameters and species composition. In particular, it is shown that an increase of both the incident light intensity or bottom nutrient concentrations favors the best light competitors, while an increase of the turbulent mixing or background turbidity favors the best nutrient competitors. These results might be important for prediction of species composition in deep ocean.     

Nutrient co-limitation of primary producer communities

Synergistic interactions between multiple limiting resources are common, highlighting the importance of co-limitation as a constraint on primary production. Our concept of resource limitation has shifted over the past two decades from an earlier paradigm of single-resource limitation towards concepts of co-limitation by multiple resources, which are predicted by various theories. Herein, we summarise multiple-resource limitation responses in plant communities using a dataset of 641 studies that applied factorial addition of nitrogen (N) and phosphorus (P) in freshwater, marine and terrestrial systems. We found that more than half of the studies displayed some type of synergistic response to N and P addition. We found support for strict definitions of co-limitation in 28% of the studies: i.e. community biomass responded to only combined N and P addition, or to both N and P when added separately. Our results highlight the importance of interactions between N and P in regulating primary producer community biomass and point to the need for future studies that address the multiple mechanisms that could lead to different types of co-limitation.     

Multiple resource limitation: nonequilibrium coexistence of species in a competition model using a synthesizing unit

During the last two decades, the simple view of resource limitation by a single resource has been changed due to the realization that co-limitation by multiple resources is often an important determinant of species growth. Hence, the multiple resource limitation hypothesis needs to be taken into account, when communities of species competing for resources are considered. We present a multiple species–multiple resource competition model which is based on the concept of synthesizing unit to formulate the growth rates of species competing for interactive essential resources. Using this model, we demonstrate that a more mechanistic explanation of interactive effects of co-limitation may lead to the known complex dynamics including nonequilibrium states as oscillations and chaos. We compare our findings with earlier investigations on biological mechanisms that can predict the outcome of multispecies competition. Moreover, we show that this model yields a periodic state where more species than limiting complementary resources can coexist (supersaturation) in a homogeneous environment. We identify two novel mechanisms, how such a state can emerge: a transcritical bifurcation of a limit cycle and a transition from a heteroclinic cycle. Furthermore, we demonstrate the robustness of the phenomenon of supersaturation when the environmental conditions are varied.     

Bottom-up and top-down drivers of herbivory on Arabica coffee along an environmental and management gradient

While sustainable agriculture relies on natural pest control, we lack insights into the relative importance of bottom-up and top-down factors on pest levels, especially along broad environmental and management gradients. To this aim, we focused on bottom-up and top-down control of herbivore damage in sixty sites in the centre of origin of Arabica coffee in southwestern Ethiopia, where coffee grows along a management gradient ranging from little or no management in the natural forest to commercial plantations. More specifically, we examined how canopy cover, percentage of surrounding forest and management intensity affected caffeine and chlorogenic acid concentration (bottom-up process) and attack of dummy caterpillars by ants and birds (top-down process), and how these in turn affected pest levels. Caffeine and chlorogenic acid concentrations were negatively related to canopy cover, while ant attack rate was positively related to canopy cover. Both ant and bird attack rate increased with the percentage of surrounding forest. Yet, secondary chemistry and caterpillar attack rates were unrelated to herbivory, and herbivory was only directly and positively affected by management intensity. Our study highlights that canopy cover can have contrasting effects on plant defence and predation, and that changes in bottom-up and top-down factors do – unlike often assumed – not necessarily translate into reduced pest levels. Instead, direct effects of management on pest levels may be more important than bottom-up or top-down mediated effects.     

Allocation tradeoffs and life histories: a conceptual and graphical framework

Tradeoffs – negative reciprocal causal relationships in net benefits between trait magnitudes – have not always been studied in depth appropriate to their central role in life‐history analysis. Here we focus on allocation tradeoffs, in which acquisition of a limiting resource requires allocation of resource to alternative traits. We identify the components of this allocation process and emphasize the importance of quantifying them. We then propose categorizing allocation tradeoffs into linear, concave and convex relationships based on the way that resource allocation yields trait magnitudes under the tradeoff. Linear relationships are over‐represented in the literature because of typically small data sets over restricted ranges of trait magnitudes, an emphasis on simple correlation analysis, and a failure to remove variation associated with acquisition of the limiting resource in characterizing the tradeoff. (We provide methods for controlling these acquisition effects.) Non‐linear relationships have been documented and are expected under plausible conditions that we summarize. We note ways that shifting environments and biological features yield plasticity of tradeoff graphs. Finally, we illustrate these points using case studies and close with priorities for future work.     

Effects of different fish species and biomass on plankton interactions in a shallow lake

Thirty-six enclosures, surface area 4 m², were placed in Little Mere, a shallow fertile lake in Cheshire, U.K. The effects of different fish species (common carp, common bream, tench and roach) of zooplanktivorous size, and their biomass (0, 200 and 700 kg ha^–1) on water chemistry, zooplankton and phytoplankton communities were investigated. Fish biomass had a strong effect on mean zooplankton size and abundance. When fish biomass rose, larger zooplankters were replaced by more numerous smaller zooplankters. Consequently phytoplankton abundance rose in the presence of higher densities of zooplanktivorous fish, as zooplankton grazing was reduced. Fish species were also significant in determining zooplankton community size structure. In enclosures with bream there were significantly greater densities of small zooplankters than in enclosures stocked with either carp, tench and, in part, roach. When carp or roach were present, the phytoplankton had a greater abundance of Cyanophyta than when bream or tench were present. Whilst top-down effects of fish predation controlled the size partitioning of the zooplankton community, this, in turn apparently controlled the bottom-up regeneration of nutrients for the phytoplankton community. At the zooplankton–phytoplankton interface, both top-down and bottom-up processes were entwined in a reciprocal feedback mechanism with the extent and direction of that relationship altered by changes in fish species. This has consequences for the way that top-down and bottom-up processes are generalised.     

Deterministic diversity changes in freshwater phytoplankton in the Yunnan–Guizhou Plateau lakes in China

Diversity measures reflect different aspects of a community, which are determined by different ecological processes. However, information is still limited on the ecological processes that are represented by different measures of species diversity. In this study, the primary driving factors for richness and diversity indices were tested. The possible ecological processes represented by each index were analyzed. First, the type of ecological process that governed the phytoplankton community in the Yunnan–Guizhou Plateau lakes, either deterministic or stochastic, was identified by Caswell's neutral model. The results indicate that a deterministic process governs the phytoplankton community. Second, the driving factors of richness and diversity indices were screened with mixed models. The results suggest that the variation of phytoplankton richness in different lakes or sites was primarily related to bottom-up factors. The variations in evenness and other measures based on the relative abundance were driven by both top-down and bottom-up factors, such as zooplankton biomass, and pH and mean light, respectively. Finally, although the different measures of diversity may respond to specific bottom-up or top-down processes, the responses to the two processes were not independent of each other. These findings will increase our understanding of the relationships between ecological processes and diversity measures for freshwater phytoplankton.     

The species composition of Antarctic phytoplankton interpreted in terms of Tilman's competition theory

Summary An attempt was made, to test for the impact of resource competition on Antarctic marine phytoplankton. According to theory, species composition near competitive equilibrium should be determined by the ratios of limiting resources. Enrichment bioassays identified silicon and nitrogen as limiting nutrients for some of the most important phytoplankton species during early austral summer in the region near the Antarctic Peninsula. Together with the generally acknowledged limiting resource light, this gave three meaningful ratios of essential resources (Si:N, Si:light, N:light) and one ratio of substitutable resources (NO₃:NH₄). Phytoplankton species assemblages were found to be well separated by the ratios of the essential resources and by mixing depth. Nine out of 12 individual species were found to be separated along at least one of the gradients of resource ratios. Where comparison with competition experiments was available, predicted and realized distributions of species were compatible.     

Bottom-Up Effects on Biomass Versus Top-Down Effects on Identity: A Multiple-Lake Fish Community Manipulation Experiment

The extent to which ecosystems are regulated by top-down relative to bottom-up control has been a dominant paradigm in ecology for many decades. For lakes, it has been shown that predation by fish is an important determinant of variation in zooplankton and phytoplankton community characteristics. Effects of fish are expected to not only be a function of total fish biomass, but also of functional composition of the fish community. Previous research on the importance of trophic cascades in lakes has largely focused on the role of zooplanktivorous and piscivorous fish. We conducted a large-scale multiple-lake fish community manipulation experiment to test for the effect of differences in fish functional community composition on the trophic structure of lakes. We examine the effect of top-down and bottom-up factors on phytoplankton and zooplankton biomass as well as on their community composition. We put our data in a broader perspective by comparing our results to data of a survey that also included ponds with low fish densities as well as ponds with very high densities of fish. Our results indicate that the overall food web structure under relative high fish densities is primarily structured by bottom-up factors, whereas community characteristics seem to be primarily regulated by top-down factors. Our results suggest a subtle interplay between bottom-up and top-down factors, in which bottom-up factors dominate in determining quantities while top-down effects are important in determining identities of the communities.     

Relative importance of top-down and bottom-up forces in food webs of Sarracenia pitcher communities at a northern and a southern site

The relative importance of resources (bottom-up forces) and natural enemies (top-down forces) for regulating food web dynamics has been debated, and both forces have been found to be critical for determining food web structure. How the relative importance of top-down and bottom-up forces varies between sites with different abiotic conditions is not well understood. Using the pitcher plant inquiline community as a model system, I examine how the relative importance of top-down and bottom-up effects differs between two disparate sites. Resources (ant carcasses) and top predators (mosquito larvae) were manipulated in two identical 4 × 4 factorial press experiments, conducted at two geographically distant sites (Michigan and Florida) within the range of the purple pitcher plant, Sarracenia purpurea, and the aquatic community that resides in its leaves. Overall, top predators reduced the density of prey populations while additional resources bolstered them, and the relative importance of top-down and bottom-up forces varied between sites and for different trophic levels. Specifically, top-down effects on protozoa were stronger in Florida than in Michigan, while the opposite pattern was found for rotifers. These findings experimentally demonstrate that the strength of predator–prey interactions, even those involving the same species, vary across space. While only two sites are compared in this study, I hypothesize that site differences in temperature, which influences metabolic rate, may be responsible for variation in consumer–resource interactions. These findings warrant further investigation into the specific factors that modify the relative importance of top-down and bottom-up effects.     

Trophic exploitation in grassland food chains: simple models and a field experiment

This study provides insight into the importance of top carnivores (top-down control) and nutrient inputs (bottom-up control) in structuring food chains in a terrestrial grassland system. Qualitative predictions about food chain structure are generated using 4 simple models, each differing in assumptions about some key component in the population dynamics of the herbivore trophic level. The four model systems can be classified broadly into two groups (1) those that assume plant resource intake by herbivores is limited by search rate and handling time as described by classic Lotka-Volterra models; and (2) those that assume plant resource intake by herbivores is limited externally by the supply rate of resources as described by alternatives to Lotka-Volterra formulations. The first class of models tends to ascribe greater importance to top-down control of food chain structure whereas the second class places greater weight on bottom-up control. I evaluated the model predictions using experimentally assembled grassland food chains in which I manipulated nutrient inputs and carnivore (wolf spider) abundance to determine the degree of top-down and bottom-up control of grassland plants and herbivores (grasshoppers). The experimental results were most consistent with predictions of the second class of models implying a predominance of bottom-up control of food chain structure.     

罗非鱼对水质的影响

鱼类是影响水库等水质的重要因素,以我国南方主要养殖鱼类之一的罗非鱼为对象,通过广东大镜山水库原位围隔实验,研究了鱼类对水质的影响。结果表明,与对照组相比罗非鱼围隔中总氮,总磷和叶绿素a浓度分别升高了42%,129%和347%。罗非鱼的排泄增加了水体营养负荷,为浮游植物生长提供大量的营养盐,引起浮游植物生物量增加,水体透明度降低。罗非鱼通过营养盐释放所产生的上行效应明显大于由其牧食导致的下行效应。     

Top-down and bottom-up controls on Dalmatian toadflax (<Emphasis Type="Italic">Linaria dalmatica</Emphasis>) performance along the Colorado Front Range,USA

Plant performance is influenced by both top-down (e.g., herbivores) and bottom-up (e.g., soil nutrients) controls. Research investigating the collective effects of such factors may provide important insight into the success and management of invasive plants. Through a combination of observational and experimental field studies, we examined top-down and bottom-up effects on the growth and reproduction of an invasive plant, Linaria dalmatica. First, we assessed attack levels and impacts of an introduced biocontrol agent, the stem-mining weevil Mecinus janthinus, on L. dalmatica plants across multiple years and sites. Then, we conducted a manipulative experiment to examine the effects of weevil attack, soil nitrogen availability, and interspecific competition on L. dalmatica. We found substantial variations in weevil attack within populations as well as across sites and years. Observational and experimental data showed that increased weevil attack was associated with a reduction in plant biomass and seed production, but only at the highest levels of attack. Nitrogen addition had a strong positive effect on plant performance, with a two-fold increase in biomass and seed production. Clipping neighboring vegetation resulted in no significant effects on L. dalmatica performance, suggesting that plants remained resource limited or continued to experienced belowground competitive effects. Overall, our research indicates that M. janthinus can exert top-down effects on L. dalmatica; however, weevil densities and attack rates observed in this study have not reached sufficient levels to yield effective control. Moreover, bottom-up controls, in particular, soil nitrogen availability, may have a large influence on the success and spread of this invasive plant.     

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.     

Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges

Phosphate (PO(4)) is an important limiting nutrient in marine environments. Marine cyanobacteria scavenge PO(4) using the high-affinity periplasmic phosphate binding protein PstS. The pstS gene has recently been identified in genomes of cyanobacterial viruses as well. Here, we analyse genes encoding transporters in genomes from viruses that infect eukaryotic phytoplankton. We identified inorganic PO(4) transporter-encoding genes from the PHO4 superfamily in several virus genomes, along with other transporter-encoding genes. Homologues of the viral pho4 genes were also identified in genome sequences from the genera that these viruses infect. Genome sequences were available from host genera of all the phytoplankton viruses analysed except the host genus Bathycoccus. Pho4 was recovered from Bathycoccus by sequencing a targeted metagenome from an uncultured Atlantic Ocean population. Phylogenetic reconstruction showed that pho4 genes from pelagophytes, haptophytes and infecting viruses were more closely related to homologues in prasinophytes than to those in what, at the species level, are considered to be closer relatives (e.g. diatoms). We also identified PHO4 superfamily members in ocean metagenomes, including new metagenomes from the Pacific Ocean. The environmental sequences grouped with pelagophytes, haptophytes, prasinophytes and viruses as well as bacteria. The analyses suggest that multiple independent pho4 gene transfer events have occurred between marine viruses and both eukaryotic and bacterial hosts. Additionally, pho4 genes were identified in available genomes from viruses that infect marine eukaryotes but not those that infect terrestrial hosts. Commonalities in marine host-virus gene exchanges indicate that manipulation of host-PO(4) uptake is an important adaptation for viral proliferation in marine systems. Our findings suggest that PO(4) -availability may not serve as a simple bottom-up control of marine phytoplankton.