Understanding stoichiometric constraints on growth using resource use efficiency imbalances.

Growth is a function of the net accrual of resources by an organism. Energy and elemental contents of organisms are dynamically linked through their uptake and allocation to biomass production, yet we lack a full understanding of how these dynamics regulate growth rate. Here, we develop a multivariate imbalance framework, the growth efficiency hypothesis, linking organismal resource contents to growth and metabolic use efficiencies, and demonstrate its effectiveness in predicting consumer growth rates under elemental and food quantity limitation. The relative proportions of carbon (%C), nitrogen (%N), phosphorus (%P), and adenosine triphosphate (%ATP) in consumers differed markedly across resource limitation treatments. Differences in their resource composition were linked to systematic changes in stoichiometric use efficiencies, which served to maintain relatively consistent relationships between elemental and ATP content in consumer tissues and optimize biomass production. Overall, these adjustments were quantitatively linked to growth, enabling highly accurate predictions of consumer growth rates.

Adaptation to a limiting element involves mitigation of multiple elemental imbalances.

About 20 elements underlie biology and thus constrain biomass production. Recent systems-level observations indicate that altered supply of one element impacts the processing of most elements encompassing an organism (i.e. ionome). Little is known about the evolutionary tendencies of ionomes as populations adapt to distinct biogeochemical environments. We evolved the bacterium Serratia marcescens under five conditions (i.e. low carbon, nitrogen, phosphorus, iron or manganese) that limited the yield of the ancestor compared with replete medium, and measured the concentrations and use efficiency of these five, and five other elements. Both physiological responses of the ancestor, as well as evolutionary responses of descendants to experimental environments involved changes in the content and use efficiencies of the limiting element, and several others. Differences in coefficients of variation in elemental contents based on biological functions were evident, with those involved in biochemical building (C, N, P, S) varying least, followed by biochemical balance (Ca, K, Mg, Na), and biochemical catalysis (Fe, Mn). Finally, descendants evolved to mitigate elemental imbalances evident in the ancestor in response to limiting conditions. Understanding the tendencies of such ionomic responses will be useful to better forecast biological responses to geochemical changes.

Revisiting the growth rate hypothesis: Towards a holistic stoichiometric understanding of growth.

The growth rate hypothesis (GRH) posits that variation in organismal stoichiometry (C:P and N:P ratios) is driven by growth-dependent allocation of P to ribosomal RNA. The GRH has found broad but not uniform support in studies across diverse biota and habitats. We synthesise information on how and why the tripartite growth-RNA-P relationship predicted by the GRH may be uncoupled and outline paths for both theoretical and empirical work needed to broaden the working domain of the GRH. We found strong support for growth to RNA (r2  = 0.59) and RNA-P to P (r2  = 0.63) relationships across taxa, but growth to P relationships were relatively weaker (r2  = 0.09). Together, the GRH was supported in ~50% of studies. Mechanisms behind GRH uncoupling were diverse but could generally be attributed to physiological (P accumulation in non-RNA pools, inactive ribosomes, translation elongation rates and protein turnover rates), ecological (limitation by resources other than P), and evolutionary (adaptation to different nutrient supply regimes) causes. These factors should be accounted for in empirical tests of the GRH and formalised mathematically to facilitate a predictive understanding of growth.

Dynamics and growth rate implications of ribosomes and mRNAs interaction in E. coli.

Understanding how cells grow and adapt under various nutrient conditions is pivotal in the study of biological stoichiometry. Recent studies provide empirical evidence that cells use multiple strategies to maintain an optimal protein production rate under different nutrient conditions. Mathematical models can provide a solid theoretical foundation that can explain experimental observations and generate testable hypotheses to further our understanding of the growth process. In this study, we generalize a modeling framework that centers on the translation process and study its asymptotic behaviors to validate algebraic manipulations involving the steady states. Using experimental results on the growth of E. coli under C-, N-, and P-limited environments, we simulate the expected quantitative measurements to show the feasibility of using the model to explain empirical evidence. Our results support the findings that cells employ multiple strategies to maintain a similar protein production rate across different nutrient limitations. Moreover, we find that the previous study underestimates the significance of certain biological rates, such as the binding rate of ribosomes to mRNA and the transition rate between different ribosomal stages. Furthermore, our simulation shows that the strategies used by cells under C- and P-limitations result in a faster overall growth dynamics than under N-limitation. In conclusion, the general modeling framework provides a valuable platform to study cell growth under different nutrient supply conditions, which also allows straightforward extensions to the coupling of transcription, translation, and energetics to deepen our understanding of the growth process.

Proteome changes in an aquatic invertebrate consumer in response to different nutritional stressors.

Nutrient imbalances in zooplankton are caused by the differences in elemental content of producers and the demand for elements in consumers, which alter the life-history traits in consumers. Changes in life-history traits are mediated through metabolic pathways that affect gene expression and the metabolome. However, less is known about proteomic changes to elemental-limitation in zooplankton. Here, we grew Daphnia pulex under high food quantity and quality (HF), low food quantity (LF), and phosphorus (P)-limited (PL) diets for six days and measured growth, elemental composition, and the proteome. Daphnids in both LF and PL diets grew less. Animals in LF diets had less carbon (C), while daphnids in PL diets had less P compared to HF fed animals. In total, we identified 1719 proteins that were used in a partial least squares regression discriminant analysis (PLS-DA). Focusing on a subset of the proteome, the PLS-DA resulted in a clear separation between animals fed HF diets and PL and LF diets. Many proteome changes in nutrient-limited diets are associated with growth, reproduction, lipid metabolism, and nutrient assimilation. Regardless of the limiting nutrient, there were less hemoglobin and small subunit processome component proteins compared to HF fed animals. Daphnids fed LF diets had less vitellogenin fused superoxide dismutase and more lipid-droplet hydrolase, whereas Daphnia fed PL diets had higher abundances of cytochrome P450 and serine protease. Our proteome results compliment other "omic" studies that could be used to study Daphnia physiology in lakes.

The complexity of co-limitation: nutrigenomics reveal non-additive interactions of calcium and phosphorus on gene expression in Daphnia pulex.

Many lakes across Canada and northern Europe have experienced declines in ambient phosphorus (P) and calcium (Ca) supply for over 20 years. While these declines might create or exacerbate nutrient limitation in aquatic food webs, our ability to detect and quantify different types of nutrient stress on zooplankton remains rudimentary. Here, we used growth bioassay experiments and whole transcriptome RNAseq, collectively nutrigenomics, to examine the nutritional phenotypes produced by low supplies of P and Ca separately and together in the freshwater zooplankter Daphnia pulex. We found that daphniids in all three nutrient-deficient categories grew slower and differed in their elemental composition. Our RNAseq results show distinct responses in singly limited treatments (Ca or P) and largely a mix of these responses in animals under low Ca and P conditions. Deeper investigation of effect magnitude and gene functional annotations reveals this patchwork of responses to cumulatively represent a co-limited nutritional phenotype. Linear discriminant analysis identified a significant separation between nutritional treatments based upon gene expression patterns with the expression patterns of just five genes needed to predict animal nutritional status with 99% accuracy. These data reveal how nutritional phenotypes are altered by individual and co-limitation of two highly important nutritional elements (Ca and P) and provide evidence that aquatic consumers can respond to limitation by more than one nutrient at a time by differentially altering their metabolism. This use of nutrigenomics demonstrates its potential to address many of the inherent complexities in studying interactions between multiple nutritional stressors in ecology and beyond.

Differential responses of macroinvertebrate ionomes across experimental N:P gradients in detritus-based headwater streams.

Diverse global change processes are reshaping the biogeochemistry of stream ecosystems. Nutrient enrichment is a common stressor that can modify flows of biologically important elements such as carbon (C), nitrogen (N), and phosphorus (P) through stream foodwebs by altering the stoichiometric composition of stream organisms. However, enrichment effects on concentrations of other important essential and trace elements in stream taxa are less understood. We investigated shifts in macroinvertebrate ionomes in response to changes in coarse benthic organic matter (CBOM) stoichiometry following N and P enrichment of five detritus-based headwater streams. Concentrations of most elements (17/19) differed among three insect genera (Maccaffertium sp., Pycnopsyche spp., and Tallaperla spp.) prior to enrichment. Genus-specific changes in the body content of: P, magnesium, and sodium (Na) in Tallaperla; P, Na, and cadmium in Pycnopsyche; and P in Maccaffertium were also found across CBOM N:P gradients. These elements increased in Tallaperla but decreased in the other two taxa due to growth dilution at larger body sizes. Multivariate elemental differences were found across all taxa, and ionome-wide shifts with dietary N and P enrichment were also observed in Tallaperla and Pycnopsyche. Our results show that macroinvertebrates exhibit distinct differences in elemental composition beyond C, N, and P and that the ionomic composition of common stream taxa can vary with body size and N and P enrichment. Thus, bottom-up changes in N and P supplies could potentially influence the cycling of lesser studied biologically essential elements in aquatic environments by altering their relative proportions in animal tissues.

The threshold elemental ratio of carbon and phosphorus of Daphnia magna and its connection to animal growth.

The growth of animal consumers is affected by the balance of elements in their diet with the transition between limitation by one element to another known as the threshold elemental ratio (TER). Precise estimates of TERs with known levels of uncertainty have yet to be generated for most zooplankton consumers. We determined the TER for carbon (C) and phosphorus (P) in for a common lake zooplankter, Daphnia magna, using experimental measurements and theoretical considerations. Daphnia growth responses to food C:P ratios across a relatively narrow range (80-350) generated an empirical estimate of TERC:P of 155 ± 14. While this TER matched our modelled estimate of TERC:P (155 ± 16), it was lower than previous estimates of this dietary transition point. No threshold was found when we examined daphnid body C:N or C:P ratios in response to changing food C:P ratios, which indicates P-limitation at even lower food C:P ratios. Our results provide strong evidence that D. magna is likely to experience acute P-limitation when food C:P ratios exceed even relatively low ratios (~155). Our model further demonstrated that while physiological adjustments may reduce the likelihood of P-limitation or reduce its intensity, these changes in animal material processing would be accompanied by reduced maximum growth rates.

Interactive effects of genotype and food quality on consumer growth rate and elemental content.

Consumer body stoichiometry is a key trait that links organismal physiology to population and ecosystem-level dynamics. However, as elemental composition has traditionally been considered to be constrained within a species, the ecological and evolutionary factors shaping consumer elemental composition have not been clearly resolved. To this end, we examined the causes and extent of variation in the body phosphorus (P) content and the expression of P-linked traits, mass specific growth rate (MSGR), and P use efficiency (PUE) of the keystone aquatic consumer Daphnia using lake surveys and common garden experiments. While daphnid body %P was relatively constrained in field assemblages sampled across an environmental P gradient, unique genotypes isolated from these lakes showed highly variable phenotypic responses when raised across dietary P gradients in the laboratory. Specifically, we observed substantial inter- and intra-specific variation and differences in daphnid responses within and among our study lakes. While variation in Daphnia body %P was mostly due to plastic phenotypic changes, we documented considerable genetic differences in daphnid MSGR and PUE, and relationships between MSGR and body P content were highly variable among genotypes. Overall, our study found that consumer responses to food quality may differ considerably among genotypes and that relationships between organismal life-history traits and body stoichiometry may be strongly influenced by genetic and environmental variation in natural assemblages.