Respiration rates in heterotrophic, free-living protozoa

Are size and mitochondrial power of cells inter-determined?

Mitochondria are the central hub of ATP production in most eukaryotic cells. Cellular power (energy per unit time), which is primarily generated in these organelles, is crucial to our understanding of cell function in health and disease. We investigated the relation between a mitochondrion's power (metabolic rate) and host cell size by combining metabolic theory with the analysis of two recent databases, one covering 109 protists and the other 63 species including protists, metazoans, microalgae, and vascular plants. We uncovered an interesting statistical regularity: in well-fed protists, relatively elevated values of mitochondrion power cluster around the smallest cell sizes and the medium-large cell sizes. In contrast, in starved protists and metazoans, the relation between mitochondrion power and cell size is inconclusive, and in microalgae and plants, mitochondrion power seems to increase from smaller cells to larger ones (where this investigation includes plant cells of volume up to ca. 2.18 × 105 μm3). Using these results, estimates are provided of the number of active ATP synthase molecules and basal uncouplers.

Gene and protein expression and metabolic flux analysis reveals metabolic scaling in liver ex vivo and in vivo

Metabolic scaling, the inverse correlation of metabolic rates to body mass, has been appreciated for more than 80 years. Studies of metabolic scaling have largely been restricted to mathematical modeling of caloric intake and oxygen consumption, and mostly rely on computational modeling. The possibility that other metabolic processes scale with body size has not been comprehensively studied. To address this gap in knowledge, we employed a systems approach including transcriptomics, proteomics, and measurement of in vitro and in vivo metabolic fluxes. Gene expression in livers of five species spanning a 30,000-fold range in mass revealed differential expression according to body mass of genes related to cytosolic and mitochondrial metabolic processes, and to detoxication of oxidative damage. To determine whether flux through key metabolic pathways is ordered inversely to body size, we applied stable isotope tracer methodology to study multiple cellular compartments, tissues, and species. Comparing C57BL/6 J mice with Sprague-Dawley rats, we demonstrate that while ordering of metabolic fluxes is not observed in in vitro cell-autonomous settings, it is present in liver slices and in vivo. Together, these data reveal that metabolic scaling extends beyond oxygen consumption to other aspects of metabolism, and is regulated at the level of gene and protein expression, enzyme activity, and substrate supply.

Temperature-dependent resistance to starvation of three contrasting freshwater ciliates

We investigated the temperature-dependent response to starvation of three contrasting freshwater ciliates (Ciliophora). The cyst-forming algivorous species Meseres corlissi and the bactivorous species Glaucomides bromelicola, which cannot form cysts, co-occur in the reservoirs (tanks) of tree bromeliads. The mixotrophic species Coleps spetai is common in many lakes. We hypothesized that the ciliates' different traits and life strategies would affect their survival rates and temperature sensitivity under food depleted conditions. We measured the decline of the ciliate populations in microcosm experiments at different temperatures for several days. We used an imaging flow cytometer to size the ciliates and documented their morphological and physiological changes in response to starvation. We found that the cyst-forming species had the highest mortality rates but may endure long-term starvation by encystment. The sympatric, non-encysting species suffered the lowest mortality rates and could survive for more than three weeks without food. The mixotrophic species had intermediate mortality rates but showed the highest phenotypic plasticity in response to starvation. A significant fraction of the C. spetai population appeared unaffected by starvation, suggesting that the endosymbionts provided some resources to the host cells. The mean mortality rate per day of all three species increased with temperature by 0.09 °C^-1.

Planktonic prey size selection reveals an emergent keystone predator effect and niche partitioning

Marine herbivorous protists are often the dominant grazers of primary production. We developed a size-based model with flexible size-based grazing to encapsulate taxonomic and behavioral diversity. We examined individual and combined grazing impacts by three consumer sizes that span the size range of protistan grazers- 5, 50, and 200 μm-on a size-structured phytoplankton community. Prey size choice and dietary niche width varied with consumer size and with co-existence of other consumers. When all consumer sizes were present, distinct dietary niches emerged, with a range of consumer-prey size ratios spanning from 25:1 to 0.4:1, encompassing the canonical 10:1 often assumed. Grazing on all phytoplankton size classes maximized the phytoplankton size diversity through the keystone predator effect, resulting in a phytoplankton spectral slope of approximately -4, agreeing with field data. This mechanistic model suggests the observed size structure of phytoplankton communities is at least in part the result of selective consumer feeding.

Energetics and evolution of anaerobic microbial eukaryotes

Mitochondria and aerobic respiration have been suggested to be required for the evolution of eukaryotic cell complexity. Aerobic respiration is several times more energetically efficient than fermentation. Moreover, aerobic respiration occurs at internalized mitochondrial membranes that are not constrained by a sublinear scaling with cell volume. However, diverse and complex anaerobic eukaryotes (for example, free-living and parasitic unicellular, and even small multicellular, eukaryotes) that exclusively rely on fermentation for energy generation have evolved repeatedly from aerobic ancestors. How do fermenting eukaryotes maintain their cell volumes and complexity while relying on such a low energy-yielding process? Here I propose that reduced rates of ATP generation in fermenting versus respiring eukaryotes are compensated for by longer cell cycles that satisfy lifetime energy demands. A literature survey and growth efficiency calculations show that fermenting eukaryotes divide approximately four to six times slower than aerobically respiring counterparts with similar cell volumes. Although ecological advantages such as competition avoidance offset lower growth rates and yields in the short term, fermenting eukaryotes inevitably have fewer physiological and ecological possibilities, which ultimately constrain their long-term evolutionary trajectories.

The role of mitochondrial energetics in the origin and diversification of eukaryotes

The origin of eukaryotic cell size and complexity is often thought to have required an energy excess supplied by mitochondria. Recent observations show energy demands to scale continuously with cell volume, suggesting that eukaryotes do not have higher energetic capacity. However, respiratory membrane area scales superlinearly with the cell surface area. Furthermore, the consequences of the contrasting genomic architectures between prokaryotes and eukaryotes have not been precisely quantified. Here, we investigated (1) the factors that affect the volumes at which prokaryotes become surface area-constrained, (2) the amount of energy divested to DNA due to contrasting genomic architectures and (3) the costs and benefits of respiring symbionts. Our analyses suggest that prokaryotes are not surface area-constrained at volumes of 10⁰‒10³ µm³, the genomic architecture of extant eukaryotes is only slightly advantageous at genomes sizes of 10⁶‒10⁷ base pairs and a larger host cell may have derived a greater advantage (lower cost) from harbouring ATP-producing symbionts. This suggests that eukaryotes first evolved without the need for mitochondria since these ranges hypothetically encompass the last eukaryotic common ancestor and its relatives. Our analyses also show that larger and faster-dividing prokaryotes would have a shortage of respiratory membrane area and divest more energy into DNA. Thus, we argue that although mitochondria may not have been required by the first eukaryotes, eukaryote diversification was ultimately dependent on mitochondria.

Evolutionary bioenergetics of ciliates

Understanding why various organisms evolve alternative ways of living requires information on both the fitness advantages of phenotypic modifications and the costs of constructing and operating cellular features. Although the former has been the subject of a myriad of ecological studies, almost no attention has been given to how organisms allocate resources to alternative structures and functions. We address these matters by capitalizing on an array of observations on diverse ciliate species and from the emerging field of evolutionary bioenergetics. A relatively robust and general estimator for the total cost of a cell per cell cycle (in units of ATP equivalents) is provided, and this is then used to understand how the magnitudes of various investments scale with cell size. Among other things, we examine the costs associated with the large macronuclear genomes of ciliates, as well as ribosomes, various internal membranes, osmoregulation, cilia, and swimming activities. Although a number of uncertainties remain, the general approach taken may serve as blueprint for expanding this line of work to additional traits and phylogenetic lineages.

Metabolic limits on classical information processing by biological cells

Biological information processing is generally assumed to be classical. Measured cellular energy budgets of both prokaryotes and eukaryotes, however, fall orders of magnitude short of the power required to maintain classical states of protein conformation and localization at the Å, fs scales predicted by single-molecule decoherence calculations and assumed by classical molecular dynamics models. We suggest that decoherence is limited to the immediate surroundings of the cell membrane and of intercompartmental boundaries within the cell, and that bulk cellular biochemistry implements quantum information processing. Detection of Bell-inequality violations in responses to perturbation of recently-separated sister cells would provide a sensitive test of this prediction. If it is correct, modeling both intra- and intercellular communication requires quantum theory.

On the power per mitochondrion and the number of associated active ATP synthases

Recent experiments and thermodynamic arguments suggest that mitochondrial temperatures are higher than those of the cytoplasm. A "hot mitochondrion" calls for a closer examination of the energy balance that endows it with these claimed elevated temperatures. As a first step in this effort, we present here a semi-quantitative bookkeeping whereby, in one stroke, a formula is proposed that yields the rate of heat production in a typical mitochondrion and a formula for estimating the number of "active" ATP synthase molecules per mitochondrion. The number of active ATP synthase molecules is the equivalent number of ATP synthases operating at 100% capacity to maintain the rate of mitochondrial heat generation. Scaling laws are shown to determine the number of active ATP synthase molecules in a mitochondrion and mitochondrial rate of heat production, whereby both appear to scale with cell volume. Four heterotrophic protozoan cell types are considered in this study. The studied cells, selected to cover a wide range of sizes (volumes) fromca.100μm³to 1 millionμm³, are estimated to exhibit a power per mitochondrion ranging fromca.1 pW to 0.03 pW. In these cells, the corresponding number of active ATP synthases per mitochondrion ranges from 5000 to just about a hundred. The absolute total number of ATP synthase molecules per mitochondrion, regardless of their activity status, can be up to two orders of magnitudes higher.

Ciliates as model organisms for the ecotoxicological risk assessment of heavy metals: A meta-analysis

Ciliates are key components of aquatic ecosystems, significantly contributing to the decomposition of organic matter and energy transfer to higher trophic levels. They are considered good biological indicators of chemical pollution and relatively sensitive to heavy metal contamination. In this study, we performed a meta-analysis of the available toxicity data of heavy metals and ciliates to assess: (1) the sensitivity of freshwater ciliates to different heavy metals, (2) the relative sensitivity of ciliates in comparison to the standard test species used in ecotoxicological risk assessment, and (3) the difference in sensitivity across ciliate taxa. Our study shows that the tolerance of ciliates to heavy metals varies notably, which is partly influenced by differences in methodological conditions across studies. Ciliates are, in general, sensitive to Mercury > Cadmium > Copper > Zinc > Lead > Chromium. Also, this study shows that most ciliates are more tolerant to heavy metal pollution than the standard test species used in ecotoxicological risk assessments, i.e., Raphidocelis subcapitata, Daphnia magna, and Onchornyncus mykiss. Threshold concentrations derived from toxicity data for these species is expected to confer sufficient protection for the vast majority of ciliate species. Our data analysis also shows that the most commonly tested ciliate species, Paramecium caudatum and Tetrahymena thermophila, are not necessarily the most sensitive ones to heavy metal pollution. Finally, this study stresses the importance of developing standard toxicity test protocols for ciliates, which could lead to a better comprehension of the toxicological impact of heavy metals and other contaminants to ciliate species.

Sub-nanowatt microfluidic single-cell calorimetry

Non-invasive and label-free calorimetry could become a disruptive technique to study single cell metabolic heat production without altering the cell behavior, but it is currently limited by insufficient sensitivity. Here, we demonstrate microfluidic single-cell calorimetry with 0.2-nW sensitivity, representing more than ten-fold enhancement over previous record, which is enabled by (i) a low-noise thermometry platform with ultralow long-term (10-h) temperature noise (80 μK) and (ii) a microfluidic channel-in-vacuum design allowing cell flow and nutrient delivery while maintaining a low thermal conductance of 2.5 μW K⁻¹. Using Tetrahymena thermophila as an example, we demonstrate on-chip single-cell calorimetry measurement with metabolic heat rates ranging from 1 to 4 nW, which are found to correlate well with the cell size. Finally, we perform real-time monitoring of metabolic rate stimulation by introducing a mitochondrial uncoupling agent to the microchannel, enabling determination of the spare respiratory capacity of the cells.

Calorimetrically measuring the heat of single cells is currently not possible due to the sensitivity of existing calorimeters. Here the authors present on-chip single cell calorimetry, with a sensitivity over ten-fold greater than the current gold-standard.

Food selectivity of anaerobic protists and direct evidence for methane production using carbon from prey bacteria by endosymbiotic methanogen

Anaerobic protists are major predators of prokaryotes in anaerobic ecosystems. However, little is known about the predation behavior of anaerobic protists because almost none have been cultured. In particular, these characteristics of anaerobic protists in the phyla Metamonada and Cercozoa have not been reported previously. In this study, we isolated three anaerobic protists, Cyclidium sp., Trichomitus sp., and Paracercomonas sp., from anaerobic granular sludge in an up-flow anaerobic sludge blanket reactor used to treat domestic sewage. Ingestion and digestion of food bacteria by anaerobic protists with or without endosymbiotic methanogens were demonstrated using tracer experiments with green fluorescent protein and a stable carbon isotope. These tracer experiments also demonstrated that Cyclidium sp. supplied CO₂ and hydrogen to endosymbiotic methanogens. While Cyclidium sp. and Trichomitus sp. ingested both Gram-negative and -positive bacteria, Paracercomonas sp. could only take up Gram-negative bacteria. Archaeal cells such as Methanobacterium beijingense and Methanospirillum hungatei did not support the growth of these protists. Metabolite patterns of all three protists differed and were influenced by food bacterial species. These reported growth rates, ingestion rates, food selectivity, and metabolite patterns provide important insights into the ecological roles of these protists in anaerobic ecosystems.

Caveats on the use of rotenone to estimate mixotrophic grazing in the oceans

Phagotrophic mixotrophs (mixoplankton) are now widely recognised as important members of food webs, but their role in the functioning of food webs is not yet fully understood. This is due to the lack of a well-established technique to estimate mixotrophic grazing. An immediate step in this direction would be the development of a method that separates mixotrophic from heterotrophic grazing that can be routinely incorporated into the common techniques used to measure microplankton herbivory (e.g., the dilution technique). This idea was explored by the addition of rotenone, an inhibitor of the respiratory electron chain that has been widely used to selectively eliminate metazoans, both in the field and in the laboratory. Accordingly, rotenone was added to auto-, mixo-, and heterotrophic protist cultures in increasing concentrations (ca. 24 h). The results showed that mixotrophs survived better than heterotrophs at low concentrations of rotenone. Nevertheless, their predation was more affected, rendering rotenone unusable as a heterotrophic grazing deterrent. Additionally, it was found that rotenone had a differential effect depending on the growth phase of an autotrophic culture. Altogether, these results suggest that previous uses of rotenone in the field may have disrupted the planktonic food web.

A Theoretical Framework for Evolutionary Cell Biology

One of the last uncharted territories in evolutionary biology concerns the link with cell biology. Because all phenotypes ultimately derive from events at the cellular level, this connection is essential to building a mechanism-based theory of evolution. Given the impressive developments in cell biological methodologies at the structural and functional levels, the potential for rapid progress is great. The primary challenge for theory development is the establishment of a quantitative framework that transcends species boundaries. Two approaches to the problem are presented here: establishing the long-term steady-state distribution of mean phenotypes under specific regimes of mutation, selection, and drift and evaluating the energetic costs of cellular structures and functions. Although not meant to be the final word, these theoretical platforms harbor potential for generating insight into a diversity of unsolved problems, ranging from genome structure to cellular architecture to aspects of motility in organisms across the Tree of Life.

Revisiting the hypothesis of an energetic barrier to genome complexity between eukaryotes and prokaryotes

The absence of genome complexity in prokaryotes, being the evolutionary precursors to eukaryotic cells comprising all complex life (the prokaryote-eukaryote divide), is a long-standing question in evolutionary biology. A previous study hypothesized that the divide exists because prokaryotic genome size is constrained by bioenergetics (prokaryotic power per gene or genome being significantly lower than eukaryotic ones). However, this hypothesis was evaluated using a relatively small dataset due to lack of data availability at the time, and is therefore controversial. Accordingly, we constructed a larger dataset of genomes, metabolic rates, cell sizes and ploidy levels to investigate whether an energetic barrier to genome complexity exists between eukaryotes and prokaryotes while statistically controlling for the confounding effects of cell size and phylogenetic signals. Notably, we showed that the differences in bioenergetics between prokaryotes and eukaryotes were less significant than those previously reported. More importantly, we found a limited contribution of power per genome and power per gene to the prokaryote-eukaryote dichotomy. Our findings indicate that the prokaryote-eukaryote divide is hard to explain from the energetic perspective. However, our findings may not entirely discount the traditional hypothesis; in contrast, they indicate the need for more careful examination.

Enzymatic origin and various curvatures of metabolic scaling in microbes

The famous and controversial power law is a basal metabolic scaling model mainly derived from the “surface rule” or a fractal transport network. However, this law neglects biological mechanisms in the important active state. Here, we hypothesized that the relative metabolic rate and growth rate of actively growing microbes are driven by the changeable rate of their rate-limiting enzymes and concluded that natural logarithmic microbial metabolism (lnλ) and growth (or biomass) (lnM) are both dependent on limiting resources, and then developed novel models with interdependence between lnλ and lnM. We tested the models using the data obtained from the literature. We explain how and why the scaling is usually curved with the difference between microbial metabolic and growth (or biomass’s) half-saturation constants (K_M, K_λ) in the active state and agree that the linear relationship of the power law is a particular case under the given condition: K_M = K_λ, which means that the enzyme dynamics may drive active and basal metabolic scaling relationships. Our interdependent model is more general than the power law, which is important for integrating the ecology and biochemical processes.

The influence of soil communities on the temperature sensitivity of soil respiration

Soil respiration represents a major carbon flux between terrestrial ecosystems and the atmosphere, and is expected to accelerate under climate warming. Despite its importance in climate change forecasts, however, our understanding of the effects of temperature on soil respiration (R_S) is incomplete. Using a metabolic ecology approach we link soil biota metabolism, community composition and heterotrophic activity to predict R_S rates across five biomes. We find that accounting for the ecological mechanisms underpinning decomposition processes predicts climatological R_S variations observed in an independent dataset (n = 312). The importance of community composition is evident because without it R_S is substantially underestimated. With increasing temperature, we predict a latitudinal increase in R_S temperature sensitivity, with Q₁₀ values ranging between 2.33 ± 0.01 in tropical forests to 2.72 ± 0.03 in tundra. This global trend has been widely observed, but has not previously been linked to soil communities.

Ocean acidification compromises a planktic calcifier with implications for global carbon cycling

Anthropogenically-forced changes in ocean chemistry at both the global and regional scale have the potential to negatively impact calcifying plankton, which play a key role in ecosystem functioning and marine carbon cycling. We cultured a globally important calcifying marine plankter (the foraminifer, Globigerina bulloides) under an ecologically relevant range of seawater pH (7.5 to 8.3 total scale). Multiple metrics of calcification and physiological performance varied with pH. At pH > 8.0, increased calcification occurred without a concomitant rise in respiration rates. However, as pH declined from 8.0 to 7.5, calcification and oxygen consumption both decreased, suggesting a reduced ability to precipitate shell material accompanied by metabolic depression. Repair of spines, important for both buoyancy and feeding, was also reduced at pH < 7.7. The dependence of calcification, respiration, and spine repair on seawater pH suggests that foraminifera will likely be challenged by future ocean conditions. Furthermore, the nature of these effects has the potential to actuate changes in vertical transport of organic and inorganic carbon, perturbing feedbacks to regional and global marine carbon cycling. The biological impacts of seawater pH have additional, important implications for the use of foraminifera as paleoceanographic indicators.

Zooplankton and the Ocean Carbon Cycle

Marine zooplankton comprise a phylogenetically and functionally diverse assemblage of protistan and metazoan consumers that occupy multiple trophic levels in pelagic food webs. Within this complex network, carbon flows via alternative zooplankton pathways drive temporal and spatial variability in production-grazing coupling, nutrient cycling, export, and transfer efficiency to higher trophic levels. We explore current knowledge of the processing of zooplankton food ingestion by absorption, egestion, respiration, excretion, and growth (production) processes. On a global scale, carbon fluxes are reasonably constrained by the grazing impact of microzooplankton and the respiratory requirements of mesozooplankton but are sensitive to uncertainties in trophic structure. The relative importance, combined magnitude, and efficiency of export mechanisms (mucous feeding webs, fecal pellets, molts, carcasses, and vertical migrations) likewise reflect regional variability in community structure. Climate change is expected to broadly alter carbon cycling by zooplankton and to have direct impacts on key species.

Influence of Starvation on Respiratory Metabolism and Pyridine Nucleotide Levels in the Marine Dinoflagellate Oxyrrhis marina

Respiratory oxygen consumption rate (RO2) and potential respiration (Φ) has been monitored during a food deprivation period in the heterotrophic dinoflagellate Oxyrrhis marina. Φ was determined by measuring the activity of the enzymes from the electron transport system (ETS), the major contributor to the oxygen consumption in the cells. Additionally, we have quantified for the first time the concentration of pyridine nucleotides in this organism, both in their oxidized (NAD(P)(+)) and reduced forms (NAD(P)H). These molecules are the main electron donors at the beginning of the ETS. We observed a dramatic decrease in RO2 within the first days, whereas Φ steadily, but more gradually declined during the entire experiment. This led to a decrease of the RO2 /Φ with time. The intracellular total pool of NAD and NADP concentration, in turn, dropped exponentially in a manner parallel to the RO2. This strong decrease was mainly driven by a reduction in the concentration of the oxidized forms. The present work constitutes a first step in clarifying the role of intracellular NAD and NADP concentrations and the redox status in the control of in vivo RO2 in marine organisms.

Respiration, growth and grazing rates of three ciliate species in hypoxic conditions

Marine hypoxic episodes are affecting both marine and freshwater bodies all over the world. Yet, limited data exists with regard to the effects of decreasing oxygen on protist metabolism. Three ciliate species were therefore isolated from Hong Kong coastal waters. Controlled hypoxic conditions were simulated in the lab environment, during which time growth, respiration and grazing rates were measured. Euplotes sp. and a Oxytrichidae-like ciliate showed decreased growth and respiration below 2.5 mg O2 L(-1), however Uronema marinum kept steady growth and respiration until below 1.5 mg O2 L(-1). Euplotes sp. and the Oxytrichidae-like ciliate had the highest ingestion rate, which dropped significantly below 3.0 mg O2 L(-1). U.marinum grazing rates were affected at and below 1.5 mg O2 L(-1), correlating with their drop in growth and respiration at this lower concentration. This study illustrates the slowing metabolism of key grazing protists, as well as species-specific tolerance in response to hypoxia.

From bacteria to piscivorous fish: estimates of whole-lake and component-specific metabolism with an ecosystem approach

The influence of functional group specific production and respiration patterns on a lake's metabolic balance remains poorly investigated to date compared to whole-system estimates of metabolism. We employed a summed component ecosystem approach for assessing lake-wide and functional group-specific metabolism (gross primary production (GPP) and respiration (R)) in shallow and eutrophic Lake Võrtsjärv in central Estonia during three years. Eleven functional groups were considered: piscivorous and benthivorous fish; phyto-, bacterio-, proto- and metazooplankton; benthic macroinvertebrates, bacteria and ciliates; macrophytes and their associated epiphytes. Metabolism of these groups was assessed by allometric equations coupled with daily records of temperature and hydrology of the lake and measurements of food web functional groups biomass. Results revealed that heterotrophy dominated most of the year, with a short autotrophic period observed in late spring. Most of the metabolism of the lake could be attributed to planktonic functional groups, with phytoplankton contributing the highest share (90% of GPP and 43% of R). A surge of protozooplankton and bacterioplankton populations forming the microbial loop caused the shift from auto- to heterotrophy in midsummer. Conversely, the benthic functional groups had overall a very small contribution to lake metabolism. We validated our ecosystem approach by comparing the GPP and R with those calculated from O2 measurements in the lake. Our findings are also in line with earlier productivity studies made with 14C or chlorophyll a (chl-a) based equations. Ideally, the ecosystem approach should be combined with diel O2 approach for investigating critical periods of metabolism shifts caused by dynamics in food-web processes.

Dispersal propensity in Tetrahymena thermophila ciliates - a reaction norm perspective

Dispersal and phenotypic plasticity are two main ways for species to deal with rapid changes of their environments. Understanding how genotypes (G), environments (E), and their interaction (genotype and environment; G × E) each affects dispersal propensity is therefore instrumental for predicting the ecological and evolutionary responses of species under global change. Here we used an actively dispersing ciliate to quantify the contributions of G, E, and G × E on dispersal propensity, exposing 44 different genotypes to three different environmental contexts (densities in isogenotype populations). Moreover, we assessed the condition dependence of dispersal, that is, whether dispersal is related to morphological, physiological, or behavioral traits. We found that genotypes showed marked differences in dispersal propensity and that dispersal is plastically adjusted to density, with the overall trend for genotypes to exhibit negative density-dependent dispersal. A small, but significant G × E interaction indicates genetic variability in plasticity and therefore some potential for dispersal plasticity to evolve. We also show evidence consistent with condition-dependent dispersal suggesting that genotypes also vary in how individual condition is linked to dispersal under different environmental contexts thereby generating complex dispersal behavior due to only three variables (genes, environment, and individual condition).

A model of proteostatic energy cost and its use in analysis of proteome trends and sequence evolution

A model of proteome-associated chemical energetic costs of cells is derived from protein-turnover kinetics and protein folding. Minimization of the proteostatic maintenance cost can explain a range of trends of proteomes and combines both protein function, stability, size, proteostatic cost, temperature, resource availability, and turnover rates in one simple framework. We then explore the ansatz that the chemical energy remaining after proteostatic maintenance is available for reproduction (or cell division) and thus, proportional to organism fitness. Selection for lower proteostatic costs is then shown to be significant vs. typical effective population sizes of yeast. The model explains and quantifies evolutionary conservation of highly abundant proteins as arising both from functional mutations and from changes in other properties such as stability, cost, or turnover rates. We show that typical hypomorphic mutations can be selected against due to increased cost of compensatory protein expression (both in the mutated gene and in related genes, i.e. epistasis) rather than compromised function itself, although this compensation depends on the protein's importance. Such mutations exhibit larger selective disadvantage in abundant, large, synthetically costly, and/or short-lived proteins. Selection against increased turnover costs of less stable proteins rather than misfolding toxicity per se can explain equilibrium protein stability distributions, in agreement with recent findings in E. coli. The proteostatic selection pressure is stronger at low metabolic rates (i.e. scarce environments) and in hot habitats, explaining proteome adaptations towards rough environments as a question of energy. The model may also explain several trade-offs observed in protein evolution and suggests how protein properties can coevolve to maintain low proteostatic cost.

Increased microbial activity in a warmer and wetter climate enhances the risk of coastal hypoxia

The coastal zone is the most productive area of the marine environment and the area that is most exposed to environmental drivers associated with human pressures in a watershed. In dark bottle incubation experiments, we investigated the short-term interactive effects of changes in salinity, temperature and riverine dissolved organic matter (rDOM) on microbial respiration, growth and abundance in an estuarine community. An interaction effect was found for bacterial growth, where the assimilation of rDOM increased at higher salinities. A 3 °C rise in the temperature had a positive effect on microbial respiration. A higher concentration of DOM consistently enhanced respiration and bacterial abundance, while an increase in temperature reduced bacterial abundance. The latter result was most likely caused by a positive interaction effect of temperature, salinity and rDOM on the abundance of bacterivorous flagellates. Elevated temperature and precipitation, causing increased discharges of rDOM and an associated lowered salinity, will therefore primarily promote bacterial respiration, growth and bacterivore abundance. Our results suggest a positive net outcome for microbial activity under the projected climate change, driven by different, partially interacting environmental factors. Thus, hypoxia in coastal zones may increase due to enhanced respiration caused by higher temperatures and rDOM discharge acting synergistically.

Effects of temperature on type approval testing of ballast water treatment systems

To limit the risk associated with invasion of habitats by exogenous species, the International Convention for the Control and Management of the Ships' Ballast Water and Sediments was adopted in February 2004 and may soon enter into force. The International Maritime Organization (IMO) has produced guidelines to assess the efficacy and reliability of Ballast Water Treatment Systems (BWTS), but no guidance on how to take temperature into account during test cycles has been provided yet. Temperature is one of the main factors influencing the distribution and ecology of organisms along latitudes. Its increase results in higher grazing, growth, and reproduction rates of zooplankton. Under dark conditions, phytoplankton loss is also increased due to faster natural decay as well as enhanced top down control from zooplankton. Increased temperatures also improve the efficacy of chemical treatment, whereas the decay rates of disinfectants and their byproducts are potentially accelerated. The IMO guidelines for the type approval of BWTS should be amended to include recommendations on how to take temperature into account. Failing to ensure comparability and reliability between tests may pose a threat to the environment and may create problems for those attempting to apply BWTS. We propose to use a fixed Q10 value and a temperature of reference to adjust the retention time in ballast water tanks during testing.

Energetics and genetics across the prokaryote-eukaryote divide

BACKGROUND

All complex life on Earth is eukaryotic. All eukaryotic cells share a common ancestor that arose just once in four billion years of evolution. Prokaryotes show no tendency to evolve greater morphological complexity, despite their metabolic virtuosity. Here I argue that the eukaryotic cell originated in a unique prokaryotic endosymbiosis, a singular event that transformed the selection pressures acting on both host and endosymbiont.

RESULTS

The reductive evolution and specialisation of endosymbionts to mitochondria resulted in an extreme genomic asymmetry, in which the residual mitochondrial genomes enabled the expansion of bioenergetic membranes over several orders of magnitude, overcoming the energetic constraints on prokaryotic genome size, and permitting the host cell genome to expand (in principle) over 200,000-fold. This energetic transformation was permissive, not prescriptive; I suggest that the actual increase in early eukaryotic genome size was driven by a heavy early bombardment of genes and introns from the endosymbiont to the host cell, producing a high mutation rate. Unlike prokaryotes, with lower mutation rates and heavy selection pressure to lose genes, early eukaryotes without genome-size limitations could mask mutations by cell fusion and genome duplication, as in allopolyploidy, giving rise to a proto-sexual cell cycle. The side effect was that a large number of shared eukaryotic basal traits accumulated in the same population, a sexual eukaryotic common ancestor, radically different to any known prokaryote.

CONCLUSIONS

The combination of massive bioenergetic expansion, release from genome-size constraints, and high mutation rate favoured a protosexual cell cycle and the accumulation of eukaryotic traits. These factors explain the unique origin of eukaryotes, the absence of true evolutionary intermediates, and the evolution of sex in eukaryotes but not prokaryotes.

REVIEWERS

This article was reviewed by: Eugene Koonin, William Martin, Ford Doolittle and Mark van der Giezen. For complete reports see the Reviewers' Comments section.

Mechanisms of temperature-dependent swimming: the importance of physics, physiology and body size in determining protist swimming speed

Body temperatures and thus physiological rates of poikilothermic organisms are determined by environmental temperature. The power an organism has available for swimming is largely dependent on physiological rates and thus body temperature. However, retarding forces such as drag are contingent on the temperature-dependent physical properties of water and on an organism's size. Consequently, the swimming ability of poikilotherms is highly temperature dependent. The importance of the temperature-dependent physical properties of water (e.g. viscosity) in determining swimming speed is poorly understood. Here we propose a semi-mechanistic model to describe how biological rates, size and the physics of the environment contribute to the temperature dependency of microbial swimming speed. Data on the swimming speed and size of a predatory protist and its protist prey were collected and used to test our model. Data were collected by manipulating both the temperature and the viscosity (independently of temperature) of the organism's environment. Protists were either cultured in their test environment (for several generations) or rapidly exposed to their test environment to assess their ability to adapt or acclimate to treatments. Both biological rates and the physics of the environment were predicted to and observed to contribute to the swimming speed of protists. Body size was not temperature dependent, and protists expressed some ability to acclimate to changes in either temperature or viscosity. Overall, using our parameter estimates and novel model, we are able to suggest that 30 to 40% (depending on species) of the response in swimming speed associated with a reduction in temperature from 20 to 5°C is due to viscosity. Because encounter rates between protist predators and their prey are determined by swimming speed, temperature- and viscosity-dependent swimming speeds are likely to result in temperature- and viscosity-dependent trophic interactions.

The energetics of genome complexity

All complex life is composed of eukaryotic (nucleated) cells. The eukaryotic cell arose from prokaryotes just once in four billion years, and otherwise prokaryotes show no tendency to evolve greater complexity. Why not? Prokaryotic genome size is constrained by bioenergetics. The endosymbiosis that gave rise to mitochondria restructured the distribution of DNA in relation to bioenergetic membranes, permitting a remarkable 200,000-fold expansion in the number of genes expressed. This vast leap in genomic capacity was strictly dependent on mitochondrial power, and prerequisite to eukaryote complexity: the key innovation en route to multicellular life.

Shifts in metabolic scaling, production, and efficiency across major evolutionary transitions of life

The diversification of life involved enormous increases in size and complexity. The evolutionary transitions from prokaryotes to unicellular eukaryotes to metazoans were accompanied by major innovations in metabolic design. Here we show that the scalings of metabolic rate, population growth rate, and production efficiency with body size have changed across the evolutionary transitions. Metabolic rate scales with body mass superlinearly in prokaryotes, linearly in protists, and sublinearly in metazoans, so Kleiber's 3/4 power scaling law does not apply universally across organisms. The scaling of maximum population growth rate shifts from positive in prokaryotes to negative in protists and metazoans, and the efficiency of production declines across these groups. Major changes in metabolic processes during the early evolution of life overcame existing constraints, exploited new opportunities, and imposed new constraints.

A mass transfer explanation of metabolic scaling relations in some aquatic invertebrates and algae

Chemical engineering theory can be used in accounting for the broad range of metabolic scaling exponents found in some aquatic invertebrates and algae. Delivery of metabolically important compounds to these organisms occurs by diffusion through a boundary layer. Dimensionless relations (Sherwood-Reynolds number functions) demonstrate the degree to which water motion and organism size affect mass transfer, and ultimately, metabolic rate. Derivation of mass exponents in the range 0.31 to 1.25 for simple geometries such as plates, spheres, and cylinders directly follows from knowledge of the Sherwood-Reynolds number relations. The range of exponents predicted is that found by allometric studies of metabolic rate in these organisms.