Partitioning the Apparent Temperature Sensitivity into Within- and Across-Taxa Responses: Revisiting the Difference between Autotrophic and Heterotrophic Protists.

AbstractConventional analyses suggest that the metabolism of heterotrophs is thermally more sensitive than that of autotrophs, implying that warming leads to pronounced trophodynamic imbalances. However, these analyses inappropriately combine within- and across-taxa trends. Our new analysis separates these, revealing that 92% of the difference in the apparent thermal sensitivity between autotrophic and heterotrophic protists does indeed arise from within-taxa responses. Fitness differences among taxa adapted to different temperature regimes only partially compensate for the positive biochemical relationship between temperature and growth rate within taxa, supporting the hotter-is-partially-better hypothesis. Our work highlights the importance of separating within- and across-taxa responses when comparing temperature sensitivities between groups, which is relevant to how trophic imbalances and carbon fluxes respond to warming.

"Surface Browsing" May Allow "Filter-Feeding" Protozoa to Exert Top-Down Control on Colony-Forming Toxic Cyanobacterial Blooms.

Blooms of the cyanobacterium Microcystis threaten aquatic ecosystems. Protozoa grazing can control unicellular Microcystis populations; however, Microcystis blooms are composed of multicellular colonies that are thought to prevent grazing. We show that this is not so: the model ciliate Paramecium has an impact on Microcystis populations through grazing, even when large colonies occur, and this leads to a corresponding decrease in toxic microcystins. Notably, as the number of large colonies increased, Paramecium exerted top-down control by altering its feeding behavior: once the colony size was >12-20 µm, Paramecium no longer acted as a "filter feeder"; instead, it became a "surface browser," grazing around and between larger colonies, removing individual Microcystis and small colonies. However, as the proportion of large colonies increased, exponentially reducing the surface area to volume ratio, the impact of Paramecium decreased exponentially. This study provides new insights into how protozoa may affect Microcystis populations through top-down control of blooms.

Ecology of planktonic ciliates in a changing world: Concepts, methods, and challenges.

Plankton ecologists ultimately focus on forecasting, both applied and environmental outcomes. We review how appreciating planktonic ciliates has become central to these predictions. We explore the 350-year-old canon on planktonic ciliates and examine its steady progression, which has been punctuated by conceptual insights and technological breakthroughs. By reflecting on this process, we offer suggestions as to where future leaps are needed, with an emphasis on predicting outcomes of global warming. We conclude that in terms of climate change research: (i) climatic hotspots (e.g. polar oceans) require attention; (ii) simply adding ciliate measurements to zooplankton/phytoplankton-based sampling programs is inappropriate; (iii) elucidating the rare biosphere's functional ecology requires culture-independent genetic methods; (iv) evaluating genetic adaptation (microevolution) and population composition shifts is required; (v) contrasting marine and freshwaters needs attention; (vi) mixotrophy needs attention; (vii) laboratory and field studies must couple automated measurements and molecular assessment of functional gene expression; (viii) ciliate trophic diversity requires appreciation; and (ix) marrying gene expression and function, coupled with climate change scenarios is needed. In short, continued academic efforts and financial support are essential to achieve the above; these will lead to understanding how ciliates will respond to climate change, providing tools for forecasting.

False Exclusion: A Case to Embed Predator Performance in Classical Population Models.

We argue that predator-prey dynamics, a cornerstone of ecology, can be driven by insufficiently explored aspects of predator performance that are inherently prey dependent: that is, these have been falsely excluded. Classical (Lotka-Volterra-based) models tend to consider only prey-dependent ingestion rate. We highlight three other prey-dependent responses and provide empirically derived functions to describe them. These functions introduce neglected nonlinearities and threshold behaviors into dynamic models, leading to unexpected outcomes: specifically, as prey abundance increases predators (1) become less efficient at using prey; (2) initially allocate resources toward survival and then allocate resources toward reproduction; and (3) are less likely to die. Based on experiments using model zooplankton, we explore the consequences of including these functions in the classical structure and show that they alter qualitative and quantitative dynamics of an empirically informed generic predator-prey model. Through bifurcation analysis, our revised structure predicts (1) predator extinctions, where the classical structure allows persistence; (2) predator survival, where the classical structure drives predators toward extinction; and (3) greater stability through smaller amplitude of cycles, relative to the classical structure. Then, by exploring parameter space, we show how these responses alter predictions of predator-prey stability and competition between predators. In light of our results, we suggest that classical assumptions about predator responses to prey abundance should be reevaluated.

Beyond the "Code": A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora).

Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigations of biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversity of ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from a workshop that explored ways to implement six Grand Challenges proposed by the International Research Coordination Network for Biodiversity of Ciliates (IRCN-BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN-BC proposes to populate The Ciliate Guide, an online database, with biodiversity-related data and metadata to create a resource that will facilitate accurate taxonomic identifications and promote sharing of data.

Did Gause Have a Yeast Infection?

We planned to develop predator-prey models using Paramecium and yeast, but they have not been empirically examined since work by Gause in the 1930s. Therefore, we evaluated if Paramecium aurelia ingests and grows on eight yeasts. Recognising that it ingested yeasts but could not grow, we assessed if it might grow on other yeasts, by empirically parameterising a predator-prey model that relies on ingestion, not growth. Simulations were compared to P. aurelia-yeast time-series data, from Gause. We hypothesised that if the model simulated predator-prey dynamics that mimicked the original data, then possibly P. aurelia could grow on yeast; simulations did not mimic the original data. Reviewing works by Gause exposed two issues: experiments were undoubtedly contaminated with bacteria, allowing growth on bacteria, not yeast; and the population cycle data cannot be considered a self-sustaining time series, as they were manipulated by adding yeast and ciliates. We conclude that past and future work should not rely on this system, for either empirical or theoretical evaluations. Finally, although we show that P. aurelia, P. caudatum, Euplotes patella, and Blepharisma sp. cannot grow on yeast, Tetrahymena pyriformis and Colpidium striatum can; these may provide models to explore predator-prey dynamics.

A legacy of contrasting spatial genetic structure on either side of the Atlantic-Mediterranean transition zone in a marine protist.

The mechanisms that underpin the varied spatial genetic structures exhibited by free-living marine microorganisms remain controversial, with most studies emphasizing a high dispersal capability that should redistribute genetic diversity in contrast to most macroorganisms whose populations often retain a genetic signature of demographic response to historic climate fluctuations. We quantified the European phylogeographic structure of the marine flagellate Oxyrrhis marina and found a marked difference in spatial genetic structure, population demography, and genetic diversity between the northwest Atlantic and Mediterranean Sea that reflects the persistent separation of these regions as well as context-dependent population responses to contrasting environments. We found similar geographic variation in the level of genetic diversity in the sister species Oxyrrhis maritima. Because the capacity for wide dispersal is not always realized, historic genetic footprints of range expansion and contraction persist in contemporary populations of marine microbes, as they do in larger species. Indeed, the well-described genetic effects of climatic variation on macroorganisms provide clear, testable hypotheses about the processes that drive genetic divergence in marine microbes and thus about the response to future environmental change.

Reconsidering the importance of the past in predator-prey models: both numerical and functional responses depend on delayed prey densities.

We propose that delayed predator-prey models may provide superficially acceptable predictions for spurious reasons. Through experimentation and modelling, we offer a new approach: using a model experimental predator-prey system (the ciliates Didinium and Paramecium), we determine the influence of past-prey abundance at a fixed delay (approx. one generation) on both functional and numerical responses (i.e. the influence of present : past-prey abundance on ingestion and growth, respectively). We reveal a nonlinear influence of past-prey abundance on both responses, with the two responding differently. Including these responses in a model indicated that delay in the numerical response drives population oscillations, supporting the accepted (but untested) notion that reproduction, not feeding, is highly dependent on the past. We next indicate how delays impact short- and long-term population dynamics. Critically, we show that although superficially the standard (parsimonious) approach to modelling can reasonably fit independently obtained time-series data, it does so by relying on biologically unrealistic parameter values. By contrast, including our fully parametrized delayed density dependence provides a better fit, offering insights into underlying mechanisms. We therefore present a new approach to explore time-series data and a revised framework for further theoretical studies.

Intermediate fragmentation per se provides stable predator-prey metapopulation dynamics.

The extent to which a landscape is fragmented affects persistence of predator-prey dynamics. Increasing fragmentation concomitantly imposes conditions that stabilise and destabilise metapopulations. For the first time, we explicitly assessed the hypothesis that intermediate levels provide optimal conditions for stability. We examine four structural changes arising from increased fragmentation: increased fragment number; decreased fragment size; increased connectedness (corridors scaled to fragment); increased fragment heterogeneity (based on connectedness). Using the model predator-prey system (Didinium-Paramecium) we support our hypothesis, by examining replicated metapopulations dynamics at five fragmentation levels. Although both species became extinct without fragmentation, prey survived at low and high levels, and both survived at intermediate levels. By examining time to extinction, maximum abundances, and population asynchrony we conclude that fragmentation produces structural heterogeneity (independent of environmental heterogeneity), which influences stability. Our analysis suggests why some theoretical, field and microcosm studies present conflicting views of fragmentation effects on population persistence.

Finding your scientific story by writing backwards.

To succeed, a scientist must write well. Substantial guidance exists on writing papers that follow the classic Introduction, Methods, Results, and Discussion (IMRaD) structure. Here, we fill a critical gap in this pedagogical canon. We offer guidance on developing a good scientific story. This valuable-yet often poorly achieved-skill can increase the impact of a study and its likelihood of acceptance. A scientific story goes beyond presenting information. It is a cohesive narrative that engages the reader by presenting and solving a problem, with a beginning, middle, and end. To create this narrative structure, we urge writers to consider starting at the end of their study, starting with writing their main conclusions, which provide the basis of the Discussion, and then work backwards: Results → Methods → refine the Discussion → Introduction → Abstract → Title. In this brief and informal editorial, we offer guidance to a wide audience, ranging from upper-level undergraduates (who have just conducted their first research project) to senior scientists (who may benefit from re-thinking their approach to writing). To do so, we provide specific instruction, examples, and a guide to the literature on how to "write backwards", linking scientific storytelling to the IMRaD structure.

The transcriptome of the novel dinoflagellate Oxyrrhis marina (Alveolata: Dinophyceae): response to salinity examined by 454 sequencing.

BACKGROUND: The heterotrophic dinoflagellate Oxyrrhis marina is increasingly studied in experimental, ecological and evolutionary contexts. Its basal phylogenetic position within the dinoflagellates make O. marina useful for understanding the origin of numerous unusual features of the dinoflagellate lineage; its broad distribution has lent O. marina to the study of protist biogeography; and nutritive flexibility and eurytopy have made it a common lab rat for the investigation of physiological responses of marine heterotrophic flagellates. Nevertheless, genome-scale resources for O. marina are scarce. Here we present a 454-based transcriptome survey for this organism. In addition, we assess sequence read abundance, as a proxy for gene expression, in response to salinity, an environmental factor potentially important in determining O. marina spatial distributions. RESULTS: Sequencing generated ~57 Mbp of data which assembled into 7, 398 contigs. Approximately 24% of contigs were nominally identified by BLAST. A further clustering of contigs (at ≥ 90% identity) revealed 164 transcript variant clusters, the largest of which (Phosphoribosylaminoimidazole-succinocarboxamide synthase) was composed of 28 variants displaying predominately synonymous variation. In a genomic context, a sample of 5 different genes were demonstrated to occur as tandem repeats, separated by short (~200-340 bp) inter-genic regions. For HSP90 several intergenic variants were detected suggesting a potentially complex genomic arrangement. In response to salinity, analysis of 454 read abundance highlighted 9 and 20 genes over or under expressed at 50 PSU, respectively. However, 454 read abundance and subsequent qPCR validation did not correlate well - suggesting that measures of gene expression via ad hoc analysis of sequence read abundance require careful interpretation. CONCLUSION: Here we indicate that tandem gene arrangements and the occurrence of multiple transcribed gene variants are common and indicate potentially complex genomic arrangements in O. marina. Comparison of the reported data set with existing O. marina and other dinoflagellates ESTs indicates little sequence overlap likely as a result of the relatively limited extent of genome scale sequence data currently available for the dinoflagellates. This is one of the first 454-based transcriptome surveys of an ancestral dinoflagellate taxon and will undoubtedly prove useful for future comparative studies aimed at reconstructing the origin of novel features of the dinoflagellates.

Porpostoma guamensis n. sp., a philasterine scuticociliate associated with brown-band disease of corals.

Brown band disease of coral is caused by a ciliate that consumes the tissue of the corals in the genus Acropora. We describe the ciliate associated with this disease on Guam, based on: general morphology, division stages, and ciliature observed on live and protargol-stained specimens; modification of the oral structures between divisional stages, observed on protargol-stained specimens; and some aspects of behavior in field and laboratory studies. Porpostoma guamensis n. sp. is elongate and has ciliature typical for the genus; live cells are 70-500 × 20-75 µm; the macronucleus is sausage-like, elongate but often bent, positioned centrally along the main cell axis; the oral ciliature follows a basic pattern, being composed of three adoral polykinetidal regions, as described for other species in the genus, although there is variability in the organization, especially in large cells where the three regions are not easily distinguished. Ciliates fed on coral with their oral region adjacent to the tissue, which they engulfed, leaving the coral a bare skeleton. Both zooxanthellae and nematocysts from coral occurred in the ciliates. Zooxanthellae appeared to be ingested alive but deteriorated within 2-3 days. Ciliates formed thin-walled division cysts on the coral and divided up to 3 times. Cysts formed around daughter cells within cysts. We provide some observations on the complex division pattern of the ciliate (i.e. tomont-trophont-cyst) and propose a possible complete pattern that requires further validation.

Prey-dependent mortality rate: a critical parameter in microbial models.

Protozoa are key components of a wide range of ecosystems, but ecological models that incorporate these microbes often suffer from poor parameterisation, specifically of top-level predator loss rates. We (1) suggest that top-level predator mortality is prey-dependent, (2) provide a novel approach to assess this response, and (3) illustrate the ecological relevance of these findings. Ciliates, Paramecium caudatum (prey) and Didinium nasutum (predator), were used to evaluate predator mortality at varying prey levels. To assess mortality, multiple (>100) predators were individually examined (in 2-ml wells), daily (for 3 days), between 0 and 120 preys ml(-1). Data were used to determine non-linear mortality and growth responses over a range of prey abundances. The responses, plus literature data were then used to parameterise a predator-prey model, based on the Rosenzweig-MacArthur structure. The model assessed the impact of variable and three levels of constant (high, average and low) mortality rates on P. caudatum-D. nasutum population dynamics. Our method to determine variable mortality rate revealed a strong concave decline in mortality with increasing prey abundance. The model indicated: (1) high- and low-constant mortality rates yielded dynamics that deviate substantially from those obtained from a variable rate; (2) average mortality rate superficially produced dynamics similar to the variable rate, but there were differences in the period of predator-prey cycles, and the lowest abundance of prey and predators (by ~2 orders of magnitude). The differences between incorporating variable and constant mortality rate indicate that including a variable rate could substantially improve microbial-based ecological models.

The protozooplankton-ichthyoplankton trophic link: an overlooked aspect of aquatic food webs.

Since the introduction of the microbial loop concept, awareness of the role played by protozooplankton in marine food webs has grown. By consuming bacteria, and then being consumed by metazooplankton, protozoa form a trophic link that channels dissolved organic material into the "classic" marine food chain. Beyond enhancing energy transfer to higher trophic levels, protozoa play a key role in improving the food quality of metazooplankton. Here, we consider a third role played by protozoa, but one that has received comparatively little attention: that as prey items for ichthyoplankton. For >100 years it has been known that fish larvae consume protozoa. Despite this, fisheries scientists and biological oceanographers still largely ignore protozoa when assessing the foodweb dynamics that regulate the growth and survival of larval fish. We review evidence supporting the importance of the protozooplankton-ichthyoplankton link, including examples from the amateur aquarium trade, the commercial aquaculture industry, and contemporary studies of larval fish. We then consider why this potentially important link continues to receive very little attention. We conclude by offering suggestions for quantifying the importance of the protozooplankton-ichthyoplankton trophic link, using both existing methods and new technologies.

Microbial Grazers May Aid in Controlling Infections Caused by the Aquatic Zoosporic Fungus Batrachochytrium dendrobatidis.

Free-living eukaryotic microbes may reduce animal diseases. We evaluated the dynamics by which micrograzers (primarily protozoa) apply top-down control on the chytrid Batrachochytrium dendrobatidis (Bd) a devastating, panzootic pathogen of amphibians. Although micrograzers consumed zoospores (∼3 µm), the dispersal stage of chytrids, not all species grew monoxenically on zoospores. However, the ubiquitous ciliate Tetrahymena pyriformis, which likely co-occurs with Bd, grew at near its maximum rate (r = 1.7 d-1). A functional response (ingestion vs. prey abundance) for T. pyriformis, measured using spore-surrogates (microspheres) revealed maximum ingestion (I max ) of 1.63 × 103 zoospores d-1, with a half saturation constant (k) of 5.75 × 103 zoospores ml-1. Using these growth and grazing data we developed and assessed a population model that incorporated chytrid-host and micrograzer dynamics. Simulations using our data and realistic parameters obtained from the literature suggested that micrograzers could control Bd and potentially prevent chytridiomycosis (defined as 104 sporangia host-1). However, simulated inferior micrograzers (0.7 × I max and 1.5 × k) did not prevent chytridiomycosis, although they ultimately reduced pathogen abundance to below levels resulting in disease. These findings indicate how micrograzer responses can be applied when modeling disease dynamics for Bd and other zoosporic fungi.

Factors controlling the abundance and size distribution of the phototrophic ciliate Myrionecta rubra in open waters of the North Atlantic.

Myrionecta rubra, a ubiquitous planktonic ciliate, has received much attention due to its wide distribution, occurrence as a red tide organism, and unusual cryptophyte endosymbiont. Although well studied in coastal waters, M. rubra is poorly examined in the open ocean. In the Irminger Basin, North Atlantic, the abundance of M. rubra was 0-5 cells/ml, which is low compared with that found in coastal areas. Distinct patchiness (100 km) was revealed by geostatistical analysis. Multiple regression indicated there was little relationship between M. rubra abundance and a number of environmental factors, with the exception of temperature and phytoplankton biomass, which influenced abundance in the spring. We also improve on studies that indicate distinct size classes of M. rubra; we statistically recognise four significantly distinct width classes (5-16, 12-23, 18-27, 21-33 microm), which decrease in abundance with increasing size. A multinomial logistic regression revealed the main variable correlated with this size distribution was ambient nitrate concentration. Finally, we propose a hypothesis for the distribution of sizes, involving nutrients, feeding, and dividing of the endosymbiont.

An evidence-based framework for predicting the impact of differing autotroph-heterotroph thermal sensitivities on consumer-prey dynamics.

Increased temperature accelerates vital rates, influencing microbial population and wider ecosystem dynamics, for example, the predicted increases in cyanobacterial blooms associated with global warming. However, heterotrophic and mixotrophic protists, which are dominant grazers of microalgae, may be more thermally sensitive than autotrophs, and thus prey could be suppressed as temperature rises. Theoretical and meta-analyses have begun to address this issue, but an appropriate framework linking experimental data with theory is lacking. Using ecophysiological data to develop a novel model structure, we provide the first validation of this thermal sensitivity hypothesis: increased temperature improves the consumer's ability to control the autotrophic prey. Specifically, the model accounts for temperature effects on auto- and mixotrophs and ingestion, growth and mortality rates, using an ecologically and economically important system (cyanobacteria grazed by a mixotrophic flagellate). Once established, we show the model to be a good predictor of temperature impacts on consumer-prey dynamics by comparing simulations with microcosm observations. Then, through simulations, we indicate our conclusions remain valid, even with large changes in bottom-up factors (prey growth and carrying capacity). In conclusion, we show that rising temperature could, counterintuitively, reduce the propensity for microalgal blooms to occur and, critically, provide a novel model framework for needed, continued assessment.

Functional ecology of aquatic phagotrophic protists - Concepts, limitations, and perspectives.

Functional ecology is a subdiscipline that aims to enable a mechanistic understanding of patterns and processes from the organismic to the ecosystem level. This paper addresses some main aspects of the process-oriented current knowledge on phagotrophic, i.e. heterotrophic and mixotrophic, protists in aquatic food webs. This is not an exhaustive review; rather, we focus on conceptual issues, in particular on the numerical and functional response of these organisms. We discuss the evolution of concepts and define parameters to evaluate predator-prey dynamics ranging from Lotka-Volterra to the Independent Response Model. Since protists have extremely versatile feeding modes, we explore if there are systematic differences related to their taxonomic affiliation and life strategies. We differentiate between intrinsic factors (nutritional history, acclimatisation) and extrinsic factors (temperature, food, turbulence) affecting feeding, growth, and survival of protist populations. We briefly consider intraspecific variability of some key parameters and constraints inherent in laboratory microcosm experiments. We then upscale the significance of phagotrophic protists in food webs to the ocean level. Finally, we discuss limitations of the mechanistic understanding of protist functional ecology resulting from principal unpredictability of nonlinear dynamics. We conclude by defining open questions and identifying perspectives for future research on functional ecology of aquatic phagotrophic protists.

Restructuring fundamental predator-prey models by recognising prey-dependent conversion efficiency and mortality rates.

Incorporating protozoa into population models (from simple predator-prey explorations to complex food web simulations) is of conceptual, ecological, and economic importance. From theoretical and empirical perspectives, we expose unappreciated complexity in the traditional predator-prey model structure and provide a parsimonious solution, especially for protistologists. We focus on how prey abundance alters two key components of models: predator conversion efficiency (e, the proportion of prey converted to predator, before mortality loss) and predator mortality (δ, the portion of the population lost though death). Using a well-established model system (Paramecium and Didinium), we collect data to parameterize a range of existing and novel population models that differ in the functional forms of e and δ. We then compare model simulations to an empirically obtained time-series of predator-prey population dynamics. The analysis indicates that prey-dependent e and δ should be considered when structuring population models and that both prey and predator biomass also vary with prey abundance. Both of these impact the ability of the model to predict population dynamics and, therefore, should be included in theoretical model evaluations and assessment of ecosystem dynamics associated with biomass flux.

Protists decrease in size linearly with temperature: ca. 2.5% degrees C(-1).

An inverse relationship between organism size and rearing temperature is widely observed in ectotherms ('the temperature-size rule', TSR). This has rarely been quantified for related taxa, and its applicability to protists also required testing. Here, we quantify the relationship between temperature and mean cell volume within the protists by a meta-analysis of published data covering marine, brackish water and freshwater autotrophs and heterotrophs. In each of 44 datasets, a linear relationship between temperature and size could not be rejected, and a negative trend was found in 32 cases (20 gave significant negative regressions, p < 0.05). By combining 65 datasets, we revealed, for each 1 degrees C increase, a cell-size reduction of 2.5% (95% CI of 1.7-3.3%) of the volume observed at 15 degrees C. The value did not differ across taxa (amoebae, ciliates, diatoms, dinoflagellates, flagellates), habitats, modes of nutrition or combinations of these. The data are consistent with two hypotheses that are capable of explaining the TSR in ectotherms generally: (i) resource, especially respiratory gas, limitation; and (ii) fitness gains from dividing earlier as population growth increases. Using the above relationship we show how changes in cell numbers with temperature can be estimated from changes in biomass and vice versa; ignoring this relationship would produce a systematic error.