Mean mass-specific metabolic rates are strikingly similar across life's major domains: Evidence for life's metabolic optimum

In-vivo quantification of electron flow through photosystem I - Cyclic electron transport makes up about 35% in a cyanobacterium

Photosynthetic electron flow, driven by photosystem I and II, provides chemical energy for carbon fixation. In addition to a linear mode a second cyclic route exists, which only involves photosystem I. The exact contributions of linear and cyclic transport are still a matter of debate. Here, we describe the development of a method that allows quantification of electron flow in absolute terms through photosystem I in a photosynthetic organism for the first time. Specific in-vivo protocols allowed to discern the redox states of plastocyanin, P700 and the FeS-clusters including ferredoxin at the acceptor site of PSI in the cyanobacterium Synechocystis sp. PCC 6803 with the near-infrared spectrometer Dual-KLAS/NIR. P700 absorbance changes determined with the Dual-KLAS/NIR correlated linearly with direct determinations of PSI concentrations using EPR. Dark-interval relaxation kinetics measurements (DIRK_PSI) were applied to determine electron flow through PSI. Counting electrons from hydrogen oxidation as electron donor to photosystem I in parallel to DIRK_PSI measurements confirmed the validity of the method. Electron flow determination by classical PSI yield measurements overestimates electron flow at low light intensities and saturates earlier compared to DIRK_PSI. Combination of DIRK_PSI with oxygen evolution measurements yielded a proportion of 35% of surplus electrons passing PSI compared to PSII. We attribute these electrons to cyclic electron transport, which is twice as high as assumed for plants. Counting electrons flowing through the photosystems allowed determination of the number of quanta required for photosynthesis to 11 per oxygen produced, which is close to published values.

The conundrum of hot mitochondria

The mitochondrion is often referred as the cellular powerhouse because the organelle oxidizes organic acids and NADH derived from nutriments, converting around 40% of the Gibbs free energy change of these reactions into ATP, the major energy currency of cell metabolism. Mitochondria are thus microscopic furnaces that inevitably release heat as a by-product of these reactions, and this contributes to body warming, especially in endotherms like birds and mammals. Over the last decade, the idea has emerged that mitochondria could be warmer than the cytosol, because of their intense energy metabolism. It has even been suggested that our own mitochondria could operate under normal conditions at a temperature close to 50 °C, something difficult to reconcile with the laws of thermal physics. Here, using our combined expertise in biology and physics, we exhaustively review the reports that led to the concept of a hot mitochondrion, which is essentially based on the development and use of a variety of molecular thermosensors whose intrinsic fluorescence is modified by temperature. Then, we discuss the physical concepts of heat diffusion, including mechanisms like phonons scattering, which occur in the nanoscale range. Although most of approaches with thermosensors studies present relatively sparse data and lack absolute temperature calibration, overall, they do support the hypothesis of hot mitochondria. However, there is no convincing physical explanation that would allow the organelle to maintain a higher temperature than its surroundings. We nevertheless proposed some research directions, mainly biological, that might help throw light on this intriguing conundrum.

Life's Energy and Information: Contrasting Evolution of Volume- versus Surface-Specific Rates of Energy Consumption

As humanity struggles to find a path to resilience amidst global change vagaries, understanding organizing principles of living systems as the pillar for human existence is rapidly growing in importance. However, finding quantitative definitions for order, complexity, information and functionality of living systems remains a challenge. Here, we review and develop insights into this problem from the concept of the biotic regulation of the environment developed by Victor Gorshkov (1935-2019). Life's extraordinary persistence-despite being a strongly non-equilibrium process-requires a quantum-classical duality: the program of life is written in molecules and thus can be copied without information loss, while life's interaction with its non-equilibrium environment is performed by macroscopic classical objects (living individuals) that age. Life's key energetic parameter, the volume-specific rate of energy consumption, is maintained within universal limits by most life forms. Contrary to previous suggestions, it cannot serve as a proxy for "evolutionary progress". In contrast, ecosystem-level surface-specific energy consumption declines with growing animal body size in stable ecosystems. High consumption by big animals is associated with instability. We suggest that the evolutionary increase in body size may represent a spontaneous loss of information about environmental regulation, a manifestation of life's algorithm ageing as a whole.

Scaling in Colloidal and Biological Networks

Scaling and dimensional analysis is applied to networks that describe various physical systems. Some of these networks possess fractal, scale-free, and small-world properties. The amount of information contained in a network is found by calculating its Shannon entropy. First, we consider networks arising from granular and colloidal systems (small colloidal and droplet clusters) due to pairwise interaction between the particles. Many networks found in colloidal science possess self-organizing properties due to the effect of percolation and/or self-organized criticality. Then, we discuss the allometric laws in branching vascular networks, artificial neural networks, cortical neural networks, as well as immune networks, which serve as a source of inspiration for both surface engineering and information technology. Scaling relationships in complex networks of neurons, which are organized in the neocortex in a hierarchical manner, suggest that the characteristic time constant is independent of brain size when interspecies comparison is conducted. The information content, scaling, dimensional, and topological properties of these networks are discussed.

Contribution of increasing plasma membrane to the energetic cost of early zebrafish embryogenesis

How do early embryos allocate the resources stored in the sperm and egg? Recently, we established isothermal calorimetry to measure heat dissipation by living zebra-fish embryos and to estimate the energetics of specific developmental events. During the reductive cleavage divisions, the rate of heat dissipation increases from ∼60 nJ · s-1 at the two-cell stage to ∼90 nJ · s-1 at the 1024-cell stage. Here we ask which cellular process(es) drive this increasing energetic cost. We present evidence that the cost is due to the increase in the total surface area of all the cells of the embryo. First, embryo volume stays constant during the cleavage stage, indicating that the increase is not due to growth. Second, the heat increase is blocked by nocodazole, which inhibits DNA replication, mitosis, and cell division; this suggests some aspect of cell proliferation contributes to these costs. Third, the heat increases in proportion to the total cell surface area rather than total cell number. Fourth, the heat increase falls within the range of the estimated costs of maintaining and assembling plasma membranes and associated proteins. Thus, the increase in total plasma membrane associated with cell proliferation is likely to contribute appreciably to the total energy budget of the embryo.

Constraining size-dependence of vegetation respiration rates

Plant autotrophic respiration is responsible for the atmospheric release of about half of all photosynthetically fixed carbon and responds to climate change in a manner different from photosynthesis. The plant mass-specific respiration rate (rA), a key parameter of the carbon cycle, has not been sufficiently constrained by observations at ecosystem or broader scales. In this study, a meta-analysis revealed a global relationship with vegetation biomass that explains 67-77% of the variance of rA across plant ages and biomes. rA decreased with increasing vegetation biomass such that annual rA was two orders of magnitude larger in fens and deserts than in mature forests. This relationship can be closely approximated by a power-law equation with a universal exponent and yields an estimated global autotrophic respiration rate of 64 ± 12 Pg C yr-1. This finding, which is phenomenologically and theoretically consistent with metabolic scaling and plant demography, provides a way to constrain the carbon-cycle components of Earth system models.

Plant respiration: Controlled by photosynthesis or biomass?

Two simplifying hypotheses have been proposed for whole-plant respiration. One links respiration to photosynthesis; the other to biomass. Using a first-principles carbon balance model with a prescribed live woody biomass turnover, applied at a forest research site where multidecadal measurements are available for comparison, we show that if turnover is fast the accumulation of respiring biomass is low and respiration depends primarily on photosynthesis; while if turnover is slow the accumulation of respiring biomass is high and respiration depends primarily on biomass. But the first scenario is inconsistent with evidence for substantial carry-over of fixed carbon between years, while the second implies far too great an increase in respiration during stand development-leading to depleted carbohydrate reserves and an unrealistically high mortality risk. These two mutually incompatible hypotheses are thus both incorrect. Respiration is not linearly related either to photosynthesis or to biomass, but it is more strongly controlled by recent photosynthates (and reserve availability) than by total biomass.

Does Cellular Metabolism from Primary Fibroblasts and Oxidative Stress in Blood Differ between Mammals and Birds? The (Lack-thereof) Scaling of Oxidative Stress

As part of mitonuclear communication, retrograde and anterograde signaling helps maintain homeostasis under basal conditions. Basal conditions, however, vary across phylogeny. At the cell-level, some mitonuclear retrograde responses can be quantified by measuring the constitutive components of oxidative stress, the balance between reactive oxygen species (ROS) and antioxidants. ROS are metabolic by-products produced by the mitochondria that can damage macromolecules by structurally altering proteins and inducing mutations in DNA, among other processes. To combat accumulating damage, organisms have evolved endogenous antioxidants and can consume exogenous antioxidants to sequester ROS before they cause cellular damage. ROS are also considered to be regulated through a retrograde signaling cascade from the mitochondria to the nucleus. These cellular pathways may have implications at the whole-animal level as well. For example, birds have higher basal metabolic rates, higher blood glucose concentration, and longer lifespans than similar sized mammals, however, the literature is divergent on whether oxidative stress is higher in birds compared with mammals. Herein, we collected literature values for whole-animal metabolism of birds and mammals. Then, we collected cellular metabolic rate data from primary fibroblast cells isolated from birds and mammals and we collected blood from a phylogenetically diverse group of birds and mammals housed at zoos and measured several parameters of oxidative stress. Additionally, we reviewed the literature on basal-level oxidative stress parameters between mammals and birds. We found that mass-specific metabolic rates were higher in birds compared with mammals. Our laboratory results suggest that cellular basal metabolism, total antioxidant capacity, circulating lipid damage, and catalase activity were significantly lower in birds compared with mammals. We found no body-size correlation on cellular metabolism or oxidative stress. We also found that most oxidative stress parameters significantly correlate with increasing age in mammals, but not in birds; and that correlations with reported maximum lifespans show different results compared with correlations with known aged birds. Our literature review revealed that basal levels of oxidative stress measurements for birds were rare, which made it difficult to draw conclusions.

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.

Casamino acids slow motility and stimulate surface growth in an extreme oligotroph

Environmental cues that regulate motility are poorly understood, but specific carbon and nitrogen sources, such as casamino acids (CAA), are known to stimulate motility in model organisms. However, natural environments are commonly more nutrient-limited than laboratory growth media, and the effect of energy-rich CAA on the motility of oligotrophic microorganisms is unknown. In this study, an extreme oligocarbotroph, Variovorax paradoxus YC1, was isolated from weathered shale rock within a disused mine level in North Yorkshire, UK. The addition of 0.1% CAA to minimal media significantly reduced the motility of YC1 after 72 h and inhibited swimming motility resulting in enhanced surface growth. We propose this response to CAA is a physiological adaptation to oligotrophy, facilitating the colonization of nutrient-rich environments.

A General Model for Seed and Seedling Respiratory Metabolism

The ontogeny of seed plants usually involves a dormant dehydrated state and the breaking of dormancy and germination, which distinguishes it from that of most organisms. Seed germination and seedling establishment are critical ontogenetic stages in the plant life cycle, and both are fueled by respiratory metabolism. However, the scaling of metabolic rate with respect to individual traits remains poorly understood. Here, we tested metabolic scaling theory during seed germination and early establishment growth using a recently developed model and empirical data collected from 41 species. The results show that (i) the mass-specific respiration rate (R_m) was weakly correlated with body mass, mass-specific N content, and mass-specific C content; (ii) R_m conformed to a single Michaelis-Menten curve as a function of tissue water content; and (iii) the central parameters in the model were highly correlated with DNA content and critical enzyme activities. The model offers new insights and a more integrative scaling theory that quantifies the combined effects of tissue water content and body mass on respiratory metabolism during early plant ontogeny.

Energy requirements, length of digestive tract compartments and body mass in six gerbilline rodents of the Negev Desert

Energy requirements of an animal are size dependent and, in this study, the average daily metabolic rate (ADMR) of six Negev Desert gerbilline rodents, ranging in body mass (m_b) from 10g to over 200g, scaled to m_b^0.57. Although gerbilline rodents are considered 'granivores', these rodents consume substantial amounts of green vegetation and the largest gerbil is a strict herbivore. We predicted that the lengths of the compartments of the digestive tract would scale allometrically to mb^0.33 and that ADMR would scale allometrically to the lengths of the compartments to the exponent of 1.73. Using log-transformed data, the length of the colon scaled to m_b^0.50 (r²_adj = 0.74; p= 0.02), of the caecum to m_b^0.45 (r²_adj=0.80; p= 0.01) and of the small intestine to m_b^0.30 (r²_adj=0.59; p < 0.05). Therefore, the exponents for the colon and caecum were higher than predicted and were close to the exponent for ADMR generated for the rodents. The absolute lengths of the colon (r²_adj=0.68; p= 0.03; slope = 0.99) and of the caecum (r²_adj=0.79; p= 0.01; slope = 1.19) were related significantly to ADMR, but of the small intestine was not (r²_adj=0.04; p=0.33; slope = 0.85). The exponents implied that the relationships were isometric and not allometric as predicted and that the rates of increase of the lengths of the intestine compartments were at the same rate as the increase in ADMR. The lengths of the colon and caecum were highly correlated between each other (r²_adj=0.98; p< 0.001; slope = 1.12) and explained most of the variation in ADMR. Green vegetation could be a nutritional bottleneck for rodents as it is bulky and, consequently, limits the dietary intake, and fermentation occurs in the caecum and colon, whereas seeds, which are compact and are digested in the small intestine, would limit intake to a much lesser degree. However, when the effect of body mass was eliminated by using residuals of the variables on body mass, only the length of the small intestine was significant (r²_adj=0.86; p< 0.005; slope = -1.33) and was related negatively to ADMR. Therefore, when effects of body size were removed, most of the variation in ADMR was explained by the length of the small intestine and implied that the length of the small intestine increased with a decrease in ADMR. A higher energy expenditure was related to a shorter small intestine and, therefore, by implication, a higher concentration of metabolizable energy yield of the diet. We also questioned whether there are differences in the morphology of the digestive tract due to differences in dietary consumption. The digestive tracts of the gerbils were not diverse and could be characterized as structurally homogenous. All the gerbils had a uni-locular, hemi-glandular stomach and the differences in the digestive tract among species did not seem to be of functional importance, but rather were related to the taxon. However, some important morpho-functional characteristics of the digestive tract emerged that apply to the whole group.

Linking scaling laws across eukaryotes

Scaling laws relating body mass to species characteristics are among the most universal quantitative patterns in biology. Within major taxonomic groups, the 4 key ecological variables of metabolism, abundance, growth, and mortality are often well described by power laws with exponents near 3/4 or related to that value, a commonality often attributed to biophysical constraints on metabolism. However, metabolic scaling theories remain widely debated, and the links among the 4 variables have never been formally tested across the full domain of eukaryote life, to which prevailing theory applies. Here we present datasets of unprecedented scope to examine these 4 scaling laws across all eukaryotes and link them to test whether their combinations support theoretical expectations. We find that metabolism and abundance scale with body size in a remarkably reciprocal fashion, with exponents near ±3/4 within groups, as expected from metabolic theory, but with exponents near ±1 across all groups. This reciprocal scaling supports "energetic equivalence" across eukaryotes, which hypothesizes that the partitioning of energy in space across species does not vary significantly with body size. In contrast, growth and mortality rates scale similarly both within and across groups, with exponents of ±1/4. These findings are inconsistent with a metabolic basis for growth and mortality scaling across eukaryotes. We propose that rather than limiting growth, metabolism adjusts to the needs of growth within major groups, and that growth dynamics may offer a viable theoretical basis to biological scaling.

Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

Dense Dwarfs versus Gelatinous Giants: The Trade-Offs and Physiological Limits Determining the Body Plan of Planktonic Filter Feeders

Most marine plankton have a high energy (carbon) density, but some are gelatinous with approximately 100 times more watery bodies. How do those distinctly different body plans emerge, and what are the trade-offs? We address this question by modeling the energy budget of planktonic filter feeders across life-forms, from micron-sized unicellular microbes such as choanoflagellates to centimeter-sized gelatinous tunicates such as salps. We find two equally successful strategies, one being small with high energy density (dense dwarf) and the other being large with low energy density (gelatinous giant). The constraint that forces large-but not small-filter feeders to be gelatinous is identified as a lower limit to the size-specific filter area, below which the energy costs lead to starvation. A further limit is found from the maximum size-specific motor force that restricts the access to optimum strategies. The quantified constraints are discussed in the context of other resource-acquisition strategies. We argue that interception feeding strategies can be accessed by large organisms only if they are gelatinous. On the other hand, organisms that use remote prey sensing do not need to be gelatinous, even if they are large.

Thermodynamic properties of microorganisms: determination and analysis of enthalpy, entropy, and Gibbs free energy of biomass, cells and colonies of 32 microorganism species

Thermodynamic analysis is an important part of chemical engineering. However, its application in biotechnology has been hampered by lack of data on thermodynamic properties of microorganism biomass. In this paper, a review was made of methods for estimation of thermodynamic properties of biomass, including standard enthalpy of combustion h_C⁰, enthalpy of formation h_f⁰, entropy s⁰, and Gibbs free energy of formation g_f⁰. These parameters were calculated on molar and mass specific basis for 32 microorganism species, including 14 bacteria, 7 yeast and 11 algae species. It was found that h_f⁰, s⁰, g_f⁰ are, respectively, similar for all the analyzed species, due to the fact that all living organisms have a common ancestor and thus a similar chemical composition. Furthermore, all the analyzed microorganisms have negative h_f⁰, originating from partial oxidation of all other elements by oxygen and nitrogen. A brief review was given of microorganism endogenous and growth metabolic rates. Finally, based on the determined thermodynamic properties, entropy of individual E. coli and Pseudomonas cells were determined and entropy of a Pseudomonas colony during its lifespan was calculated and analyzed. Three periods can be distinguished in the existence of a microorganism colony: (a) accumulation period when cell number, mass and entropy increase, (b) steady state period when they are approximately constant, and (c) decumulation period when they decrease.

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.

Evidence for hormonal control of heart regenerative capacity during endothermy acquisition

Tissue regenerative potential displays striking divergence across phylogeny and ontogeny, but the underlying mechanisms remain enigmatic. Loss of mammalian cardiac regenerative potential correlates with cardiomyocyte cell-cycle arrest and polyploidization as well as the development of postnatal endothermy. We reveal that diploid cardiomyocyte abundance across 41 species conforms to Kleiber's law-the ¾-power law scaling of metabolism with bodyweight-and inversely correlates with standard metabolic rate, body temperature, and serum thyroxine level. Inactivation of thyroid hormone signaling reduces mouse cardiomyocyte polyploidization, delays cell-cycle exit, and retains cardiac regenerative potential in adults. Conversely, exogenous thyroid hormones inhibit zebrafish heart regeneration. Thus, our findings suggest that loss of heart regenerative capacity in adult mammals is triggered by increasing thyroid hormones and may be a trade-off for the acquisition of endothermy.

Heat Oscillations Driven by the Embryonic Cell Cycle Reveal the Energetic Costs of Signaling

All living systems function out of equilibrium and exchange energy in the form of heat with their environment. Thus, heat flow can inform on the energetic costs of cellular processes, which are largely unknown. Here, we have repurposed an isothermal calorimeter to measure heat flow between developing zebrafish embryos and the surrounding medium. Heat flow increased over time with cell number. Unexpectedly, a prominent oscillatory component of the heat flow, with periods matching the synchronous early reductive cleavage divisions, persisted even when DNA synthesis and mitosis were blocked by inhibitors. Instead, the heat flow oscillations were driven by the phosphorylation and dephosphorylation reactions catalyzed by the cell-cycle oscillator, the biochemical network controlling mitotic entry and exit. We propose that the high energetic cost of cell-cycle signaling reflects the significant thermodynamic burden of imposing accurate and robust timing on cell proliferation during development.

Energetic equivalence underpins the size structure of tree and phytoplankton communities

The size structure of autotroph communities – the relative abundance of small vs. large individuals – shapes the functioning of ecosystems. Whether common mechanisms underpin the size structure of unicellular and multicellular autotrophs is, however, unknown. Using a global data compilation, we show that individual body masses in tree and phytoplankton communities follow power-law distributions and that the average exponents of these individual size distributions (ISD) differ. Phytoplankton communities are characterized by an average ISD exponent consistent with three-quarter-power scaling of metabolism with body mass and equivalence in energy use among mass classes. Tree communities deviate from this pattern in a manner consistent with equivalence in energy use among diameter size classes. Our findings suggest that whilst universal metabolic constraints ultimately underlie the emergent size structure of autotroph communities, divergent aspects of body size (volumetric vs. linear dimensions) shape the ecological outcome of metabolic scaling in forest vs. pelagic ecosystems.

Given the size differences between the autotrophs in aquatic and terrestrial systems, it is unclear whether the same metabolic scaling patterns apply in both groups. Here the authors unify previous datasets and show that plankton and trees follow similar power-law scaling of individual size distributions.

Body size-dependent energy storage causes Kleiber's law scaling of the metabolic rate in planarians

Kleiber's law, or the 3/4 -power law scaling of the metabolic rate with body mass, is considered one of the few quantitative laws in biology, yet its physiological basis remains unknown. Here, we report Kleiber's law scaling in the planarian Schmidtea mediterranea. Its reversible and life history-independent changes in adult body mass over 3 orders of magnitude reveal that Kleiber's law does not emerge from the size-dependent decrease in cellular metabolic rate, but from a size-dependent increase in mass per cell. Through a combination of experiment and theoretical analysis of the organismal energy balance, we further show that the mass allometry is caused by body size dependent energy storage. Our results reveal the physiological origins of Kleiber's law in planarians and have general implications for understanding a fundamental scaling law in biology.

Metabolic physiology explains macroevolutionary trends in the melanic colour system across amniotes

Metabolism links organisms to their environment through its effects on thermoregulation, feeding behaviour and energetics. Genes involved in metabolic processes have known pleiotropic effects on some melanic colour traits. Understanding links between physiology and melanic colour is critical for understanding the role of, and potential constraints on, colour production. Despite considerable variation in metabolic rates and presumed ancestral melanic coloration in vertebrates, few studies have looked at a potential relationship between these two systems in a comparative framework. Here, we test the hypothesis that changes in melanosome shape in integumentary structures track metabolic rate variation across amniotes. Using multivariate comparative analyses and incorporating both extant and fossil taxa, we find significantly faster rates of melanosome shape evolution in taxa with high metabolic rates, as well as both colour- and clade-specific differences in the relationship between metabolic rate and melanosome shape. Phylogenetic tests recover an expansion in melanosome morphospace in maniraptoran dinosaurs, as well as rate shifts within birds (in songbirds) and mammals. These findings indicate another core phenotype influenced by metabolic changes in vertebrates. They also provide a framework for testing clade-specific gene expression patterns in the melanocortin system and may improve colour reconstructions in extinct taxa.

Pyramids and cascades: a synthesis of food chain functioning and stability

Food chain theory is one of the cornerstones of ecology, providing many of its basic predictions, such as biomass pyramids, trophic cascades and predator-prey oscillations. Yet, ninety years into this theory, the conditions under which these patterns may occur and persist in nature remain subject to debate. Rather than address each pattern in isolation, we propose that they must be understood together, calling for synthesis in a fragmented landscape of theoretical and empirical results. As a first step, we propose a minimal theory that combines the long-standing energetic and dynamical approaches of food chains. We chart theoretical predictions on a concise map, where two main regimes emerge: across various functioning and stability metrics, one regime is characterised by pyramidal patterns and the other by cascade patterns. The axes of this map combine key physiological and ecological variables, such as metabolic rates and self-regulation. A quantitative comparison with data sheds light on conflicting theoretical predictions and empirical puzzles, from size spectra to causes of trophic cascade strength. We conclude that drawing systematic connections between various existing approaches to food chains, and between their predictions on functioning and stability, is a crucial step in confronting this theory to real ecosystems.

A widespread thermodynamic effect, but maintenance of biological rates through space across life's major domains

For over a century, the hypothesis of temperature compensation, the maintenance of similar biological rates in species from different thermal environments, has remained controversial. An alternative idea, that fitness is greater at higher temperatures (the thermodynamic effect), has gained increasing traction. This alternative hypothesis is also being used to understand large-scale biodiversity responses to environmental change. Yet evidence in favour of each of these contrasting hypotheses continues to emerge. In consequence, the fundamental nature of organismal thermal responses and its implications remain unresolved. Here, we investigate these ideas explicitly using a global dataset of 619 observations of four categories of organismal performance, spanning 14 phyla and 403 species. In agreement with both hypotheses, we show a positive relationship between the temperature of maximal performance rate (Topt) and environmental temperature (Tenv) for developmental rate and locomotion speed, but not growth or photosynthesis rate. Next, we demonstrate that relationships between Tenv and the maximal performance rate (Umax) are rarely significant and positive, as expected if a thermodynamic effect predominates. By contrast, a positive relationship between Topt and Umax is always present, but markedly weaker than theoretically predicted. These outcomes demonstrate that while some form of thermodynamic effect exists, ample scope is present for biochemical and physiological adaptation to thermal environments in the form of temperature compensation.

Body size and temperature effects on standard metabolic rate for determining metabolic scope for activity of the polychaete Hediste (Nereis) diversicolor

Considering the ecological importance and potential value of Hediste diversicolor, a better understanding of its metabolic rate and potential growth rates is required. The aims of this study are: (i) to describe key biometric relationships; (ii) to test the effects of temperature and body size on standard metabolic rate (as measure by oxygen consumption) to determine critical parameters, namely Arrhenius temperature (T_A ), allometric coefficient (b) and reaction rate; and (iii) to determine the metabolic scope for activity (MSA) of H. diversicolor for further comparison with published specific growth rates. Individuals were collected in a Mediterranean lagoon (France). After 10 days of acclimatization, 7 days at a fixed temperature and 24 h of fasting, resting oxygen consumption rates (VO₂ ) were individually measured in the dark at four different temperatures (11, 17, 22 and 27 °C) in worms weighing from 4 to 94 mgDW (n = 27 per temperature). Results showed that DW and L3 were the most accurate measurements of weight and length, respectively, among all the metrics tested. Conversion of WW (mg), DW (mg) and L3 (mm) were quantified with the following equations: DW = 0.15 × WW, L3 = 0.025 × TL(mm) + 1.44 and DW = 0.8 × L3^3.68. Using an equation based on temperature and allometric effects, the allometric coefficient (b) was estimated at 0.8 for DW and at 2.83 for L3. The reaction rate (VO₂ ) equaled to 12.33 µmol gDW^-1 h^-1 and 0.05 µmol mm L3^-1 h^-1 at the reference temperature (20 °C, 293.15 K). Arrhenius temperature (T_A ) was 5,707 and 5,664 K (for DW and L3, respectively). Metabolic scope for activity ranged from 120.1 to 627.6 J gDW^-1 d^-1. Predicted maximum growth rate increased with temperature, with expected values of 7-10% in the range of 15-20 °C. MSA was then used to evaluate specific growth rates (SGR) in several experiments. This paper may be used as a reference and could have interesting applications in the fields of aquaculture, ecology and biogeochemical processes.

Metabolic rates are significantly lower in abyssal Holothuroidea than in shallow-water Holothuroidea

Recent analyses of metabolic rates in fishes, echinoderms, crustaceans and cephalopods have concluded that bathymetric declines in temperature- and mass-normalized metabolic rate do not result from resource-limitation (e.g. oxygen or food/chemical energy), decreasing temperature or increasing hydrostatic pressure. Instead, based on contrasting bathymetric patterns reported in the metabolic rates of visual and non-visual taxa, declining metabolic rate with depth is proposed to result from relaxation of selection for high locomotory capacity in visual predators as light diminishes. Here, we present metabolic rates of Holothuroidea, a non-visual benthic and benthopelagic echinoderm class, determined in situ at abyssal depths (greater than 4000 m depth). Mean temperature- and mass-normalized metabolic rate did not differ significantly between shallow-water (less than 200 m depth) and bathyal (200-4000 m depth) holothurians, but was significantly lower in abyssal (greater than 4000 m depth) holothurians than in shallow-water holothurians. These results support the dominance of the visual interactions hypothesis at bathyal depths, but indicate that ecological or evolutionary pressures other than biotic visual interactions contribute to bathymetric variation in holothurian metabolic rates. Multiple nonlinear regression assuming power or exponential models indicates that in situ hydrostatic pressure and/or food/chemical energy availability are responsible for variation in holothurian metabolic rates. Consequently, these results have implications for modelling deep-sea energetics and processes.

Are the surface areas of the gills and body involved with changing metabolic scaling with temperature?

The metabolic-level boundaries (MLB) hypothesis proposes that metabolic level mediates the relative influence of surface area (SA)- versus volume-related metabolic processes on the body-mass scaling of metabolic rate in organisms. The variation in the scaling of SA may affect how metabolic level affects the metabolic scaling exponent. This study aimed to determine the influence of increasing metabolic level at a higher temperature on the metabolic scaling exponent of the goldfish and determine the link between metabolic scaling exponents and SA parameters of both gills and body. The SA of gills and body and the resting metabolic rate (RMR) of the goldfish were assessed at 15°C and 25°C, and their mass scaling exponents were analyzed. The results showed a significantly higher RMR, with a lower scaling exponent, in the goldfish at a higher temperature. The SA of the gills and the total SA of the fish (TSA) were reduced with the increasing temperature. The scaling exponent of RMR (b_RMR) tended to be close to that of the TSA at a higher temperature. This suggests that temperature positively affects metabolic level but negatively affects b_RMR The findings support the MLB hypothesis. The lower scaling exponent at a higher temperature can be alternatively explained as follows: the higher viscosity of cold water impedes respiratory ventilation and oxygen uptake and reduces metabolic rate more in smaller individuals than in larger individuals at lower temperature, thus resulting in a negative association between temperature and b_RMR.

Adaptive diversification of growth allometry in the plant Arabidopsis thaliana

Seed plants vary tremendously in size and morphology; however, variation and covariation in plant traits may be governed, at least in part, by universal biophysical laws and biological constants. Metabolic scaling theory (MST) posits that whole-organismal metabolism and growth rate are under stabilizing selection that minimizes the scaling of hydrodynamic resistance and maximizes the scaling of resource uptake. This constrains variation in physiological traits and in the rate of biomass accumulation, so that they can be expressed as mathematical functions of plant size with near-constant allometric scaling exponents across species. However, the observed variation in scaling exponents calls into question the evolutionary drivers and the universality of allometric equations. We have measured growth scaling and fitness traits of 451 Arabidopsis thaliana accessions with sequenced genomes. Variation among accessions around the scaling exponent predicted by MST was correlated with relative growth rate, seed production, and stress resistance. Genomic analyses indicate that growth allometry is affected by many genes associated with local climate and abiotic stress response. The gene with the strongest effect, PUB4, has molecular signatures of balancing selection, suggesting that intraspecific variation in growth scaling is maintained by opposing selection on the trade-off between seed production and abiotic stress resistance. Our findings suggest that variation in allometry contributes to local adaptation to contrasting environments. Our results help reconcile past debates on the origin of allometric scaling in biology and begin to link adaptive variation in allometric scaling to specific genes.

Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker

It is commonly assumed that mitochondrial DNA (mtDNA) evolves at a faster rate than nuclear DNA (nuDNA) in animals. This has contributed to the popularity of mtDNA as a molecular marker in evolutionary studies. Analyzing 121 multilocus data sets and four phylogenomic data sets encompassing 4,676 species of animals, we demonstrate that the ratio of mitochondrial over nuclear mutation rate is highly variable among animal taxa. In nonvertebrates, such as insects and arachnids, the ratio of mtDNA over nuDNA mutation rate varies between 2 and 6, whereas it is above 20, on average, in vertebrates such as scaled reptiles and birds. Interestingly, this variation is sufficient to explain the previous report of a similar level of mitochondrial polymorphism, on average, between vertebrates and nonvertebrates, which was originally interpreted as reflecting the effect of pervasive positive selection. Our analysis rather indicates that the among-phyla homogeneity in within-species mtDNA diversity is due to a negative correlation between mtDNA per-generation mutation rate and effective population size, irrespective of the action of natural selection. Finally, we explore the variation in the absolute per-year mutation rate of both mtDNA and nuDNA using a reduced data set for which fossil calibration is available, and discuss the potential determinants of mutation rate variation across genomes and taxa. This study has important implications regarding DNA-based identification methods in predicting that mtDNA barcoding should be less reliable in nonvertebrates than in vertebrates.

Macroinvertebrate identity mediates the effects of litter quality and microbial conditioning on leaf litter recycling in temperate streams

Plant litter decomposition is an essential ecosystem function that contributes to carbon and nutrient cycling in streams. Aquatic shredders, mainly macroinvertebrates, can affect this process in various ways; they consume leaf litter, breaking it down into fragments and creating suitable habitats or resources for other organisms through the production of fine particulate organic matter (FPOM). However, measures of litter-feeding traits across a wide range of aquatic macroinvertebrates are still rare. Here, we assessed the contributions of 11 species of freshwater macroinvertebrates to litter decomposition, by measuring consumption rate, FPOM production, and assimilation rate of highly decomposable (Alnus glutinosa) or poorly decomposable (Quercus robur) leaf litter types. In general, an increase in the quality of litter improved the litter consumption rate, and fungal conditioning of the leaf litter increased both the litter consumption rate and FPOM production. Macroinvertebrates specializing in leaf litter consumption also appeared to be the most sensitive to shifts in litter quality and the conditioning process. Contrary to expectations, the conditioning process did not increase the assimilation of low-quality litter. There was a strong correlation between the relative consumption rate (RCR) of the two litter types, and the relative FPOM production (RFP) was strongly correlated to the RCR. These findings suggest a consistent relationship between RCR and macroinvertebrate identity that is not affected by litter quality, and that the RFP could be inferred from the RCR. The varying responses of the macroinvertebrate feeding traits to litter quality and the conditioning process suggest that the replacement of a shredder invertebrate species by another species could have major consequences for the decomposition process and the detritus-based food web in streams. Further studies onto the importance of invertebrate identity and the effects of litter quality in a variety of freshwater ecosystems are needed to understand the whole ecosystem functioning and to predict its response to environmental changes.

Substrate-Limited and -Unlimited Coastal Microbial Communities Show Different Metabolic Responses with Regard to Temperature

Bacteria are the principal consumers of dissolved organic carbon (DOC) in the ocean and predation of bacteria makes organic carbon available to higher trophic levels. The efficiency with which bacteria convert the consumed carbon (C) into biomass (i.e., carbon growth efficiency, Y) determines their ecological as well as biogeochemical role in marine ecosystems. Yet, it is still unclear how changes in temperature will affect Y and, hence, the transfer of consumed C to higher trophic levels. Here, we experimentally investigated the effect of temperature on metabolic functions of coastal microbial communities inoculated in both nutrient-limited chemostats and nutrient–unlimited turbidostats. We inoculated chemostats and turbidostats with coastal microbial communities into seawater culture medium augmented with 20 and 100 μmol L⁻¹ of glucose respectively and measured CO₂ production, carbon biomass and cell abundance. Chemostats were cultured between 14 and 26°C and specific growth rates (μ) between 0.05 and 6.0 day⁻¹, turbidostats were cultured between 10 and 26°C with specific growth rates ranging from 28 to 62 day⁻¹. In chemostats under substrate limitation, which is common in the ocean, the specific respiration rate (r, day⁻¹) showed no trend with temperature and was roughly proportional to μ, implying that carbon growth efficiency (Y) displayed no tendency with temperature. The response was very different in turbidostats under temperature-limited, nutrient-repleted growth, here μ increased with temperature but r decreased resulting in an increase of Y with temperature (Q₁₀: 2.6). Comparison of our results with data from the literature on the respiration rate and cell weight of monospecific bacteria indicates that in general the literature data behaved similar to chemostat data, showing no trend in specific respiration with temperature. We conclude that respiration rates of nutrient-limited bacteria measured at a certain temperature cannot be adjusted to different temperatures with a temperature response function similar to Q₁₀ or Arrhenius. However, the cellular respiration rate and carbon demand rate (both: mol C cell⁻¹ day⁻¹) show statistically significant relations with cellular carbon content (mol C cell⁻¹) in chemostats, turbidostats, and the literature data.

The natural selection of metabolism and mass selects lifeforms from viruses to multicellular animals

I show that the natural selection of metabolism and mass can select for the major life‐history and allometric transitions that define lifeforms from viruses, over prokaryotes and larger unicells, to multicellular animals. The proposed selection is driven by a mass‐specific metabolism that is selected as the pace of the resource handling that generates net energy for self‐replication. An initial selection of mass is given by a dependence of mass‐specific metabolism on mass in replicators that are close to a lower size limit. A sublinear maximum dependence selects for virus‐like replicators, with no intrinsic metabolism, no cell, and practically no mass. A superlinear dependence selects for prokaryote‐like self‐replicating cells, with asexual reproduction and incomplete metabolic pathways. These self‐replicators have selection for increased net energy, and this generates a gradual unfolding of population‐dynamic feed‐back selection from interactive competition. The incomplete feed‐back selects for larger unicells with more developed metabolic pathways, and the completely developed feed‐back for multicellular animals with sexual reproduction. This model unifies the natural selection of lifeforms from viruses to multicellular animals, and it provides a parsimonious explanation where allometries and major life histories evolve from the natural selection of metabolism and mass.

Do Performance-Safety Tradeoffs Cause Hypometric Metabolic Scaling in Animals?

Hypometric scaling of aerobic metabolism in animals has been widely attributed to constraints on oxygen (O₂) supply in larger animals, but recent findings demonstrate that O₂ supply balances with need regardless of size. Larger animals also do not exhibit evidence of compensation for O₂ supply limitation. Because declining metabolic rates (MRs) are tightly linked to fitness, this provides significant evidence against the hypothesis that constraints on supply drive hypometric scaling. As an alternative, ATP demand might decline in larger animals because of performance-safety tradeoffs. Larger animals, which typically reproduce later, exhibit risk-reducing strategies that lower MR. Conversely, smaller animals are more strongly selected for growth and costly neurolocomotory performance, elevating metabolism.

Major evolutionary transitions of life, metabolic scaling and the number and size of mitochondria and chloroplasts

We investigate the effects of trophic lifestyle and two types of major evolutionary transitions in individuality-the endosymbiotic acquisition of organelles and development of multicellularity-on organellar and cellular metabolism and allometry. We develop a quantitative framework linking the size and metabolic scaling of eukaryotic cells to the abundance, size and metabolic scaling of mitochondria and chloroplasts and analyse a newly compiled, unprecedented database representing unicellular and multicellular cells covering diverse phyla and tissues. Irrespective of cellularity, numbers and total volumes of mitochondria scale linearly with cell volume, whereas chloroplasts scale sublinearly and sizes of both organelles remain largely invariant with cell size. Our framework allows us to estimate the metabolic scaling exponents of organelles and cells. Photoautotrophic cells and organelles exhibit photosynthetic scaling exponents always less than one, whereas chemoheterotrophic cells and organelles have steeper respiratory scaling exponents close to one. Multicellularity has no discernible effect on the metabolic scaling of organelles and cells. In contrast, trophic lifestyle has a profound and uniform effect, and our results suggest that endosymbiosis fundamentally altered the metabolic scaling of free-living bacterial ancestors of mitochondria and chloroplasts, from steep ancestral scaling to a shallower scaling in their endosymbiotic descendants.

Allometric scaling in-vitro

About two decades ago, West and coworkers established a model which predicts that metabolic rate follows a three quarter power relationship with the mass of an organism, based on the premise that tissues are supplied nutrients through a fractal distribution network. Quarter power scaling is widely considered a universal law of biology and it is generally accepted that were in-vitro cultures to obey allometric metabolic scaling, they would have more predictive potential and could, for instance, provide a viable substitute for animals in research. This paper outlines a theoretical and computational framework for establishing quarter power scaling in three-dimensional spherical constructs in-vitro, starting where fractal distribution ends. Allometric scaling in non-vascular spherical tissue constructs was assessed using models of Michaelis Menten oxygen consumption and diffusion. The models demonstrate that physiological scaling is maintained when about 5 to 60% of the construct is exposed to oxygen concentrations less than the Michaelis Menten constant, with a significant concentration gradient in the sphere. The results have important implications for the design of downscaled in-vitro systems with physiological relevance.

Drivers of Bacterial Maintenance and Minimal Energy Requirements

Microbes maintain themselves through a variety of processes. Several of these processes can be reduced or shut down entirely when resource availability declines. In pure culture conditions with ample substrate supply, a relationship between the maximum growth rate and the energy invested in maintenance has been reported widely. However, at the other end of the resources spectrum, bacteria are so extremely limited by energy that no growth occurs and metabolism is constrained to the most essential functions only. These minimum energy requirements have been called the basal power requirement. While seemingly different from each other, both aspects are likely components of a continuum of regulated maintenance processes. Here, we analyze cross-species tradeoffs in cellular physiology over the range of bacterial size and energy expenditure and determine the contributions to maintenance metabolism at each point along the size-energy spectrum. Furthermore, by exploring the simplest bacteria within this framework– which are most affected by maintenance constraints– we uncover which processes become most limiting. For the smallest species, maintenance metabolism converges on total metabolism, where we predict that maintenance is dominated by the repair of proteins. For larger species the relative costs of protein repair decrease and maintenance metabolism is predicted to be dominated by the repair of RNA components. These results provide new insights into which processes are likely to be regulated in environments that are extremely limited by energy.