Are you what you eat? Physiological constraints on organismal stoichiometry in an elementally imbalanced world

The relative supply of energy and elements available to organisms in the environment has strong effects on their physiology, which, in turn, can alter important ecological processes. Here we consider how resource imbalances affect three basic physiological processes common to all organisms: elemental uptake, incorporation, and release. We review recent research that addresses these core issues (uptake, incorporation, and release) as they relate to elemental homeostasis in autotrophs and heterotrophs. Our review shows the importance that organism elemental homeostasis plays in determining the types of physiological processes used to acquire, assemble, store, and release biogenic elements, which are found in widely varying ratios in the environment. Future research should examine the degree to which organisms assess their internal nutritional composition and that of their food sources within a multiple elemental and biochemical context. Also, scientists should explore if and how the stoichiometry of cellular and molecular responses underlying nutrient (elemental and biochemical) acquisition, incorporation, and release depends on the nutritional composition of food resources. These types of queries will further improve our understanding of the physiological processing of primary elements involved in growth, reproduction, and maintenance of organisms.     

Are fish what they eat? A fatty acid’s perspective

Fish are the main source of long-chain polyunsaturated fatty acids (LC-PUFA, >C₁₈) for human consumption. In general, it has been widely observed that the fatty acid (FA) profiles of farmed fish are reflective of the diet. However, the degree of tissue FA “distortion” based on incorporation of different dietary FA into fish tissues varies greatly depending on FA type, fish species and environmental factors. In terms of fish FA composition, this variation has not been comprehensively reviewed, raising the question: “Are fish what they eat?”. To date, this remains unanswered in detail. To this end, the present review quantitatively summarized the ‘diet-fish’ FA relationship via an analysis of FA composition in diets and fish tissues from 290 articles published between 1998 and 2018. Comparison of this relationship among different fish species, tissue types or individual FA was summarized. Furthermore, the influence of environmental factors such as temperature and salinity, as well as of experimental conditions such as fish size and trophic level, feeding duration, and dietary lipid level on this relationship are discussed herein. Moreover, as a means of restoring LC-PUFA in fish, an emphasis was paid to the fish oil finishing strategy after long-term feeding with alternative lipid sources. It is envisaged that the present review will be beneficial in providing a more comprehensive understanding of the fundamental relationship between the FA composition in diets, and subsequently, in the farmed fish. Such information is integral to maintaining the quality of farmed fish fillets from the perspective of FA composition.     

Are you what you eat? Effects of trophic discrimination factors on estimates of food assimilation and trophic position with a new estimation method

A key factor for estimates of assimilation of resources and trophic position based on stable isotope data is the trophic discrimination factor (TDF). TDFs are assumed based on literature reviews, but may vary depending on a variety of factors, including the type of diet. We analyzed effects of alternative TDFs on estimates of assimilated resources and trophic positions for an omnivorous fish, Jenynsia multidentata, that reveals dietary variation among locations across a salinity gradient of a coastal lagoon in southern Brazil. We also compared estimates of foods ingested vs. foods assimilated. Food assimilation was estimated using carbon (δ¹³C) and nitrogen (δ¹⁵N) stable isotope ratios of food sources and consumer muscle tissue and an isotopic mixing model (SIAR); consumer trophic position (TP) was estimated from consumer and production source δ¹⁵N values. Diet was estimated using an index of relative importance based on frequency of occurrence and volumetric and numeric proportions of food items from stomach contents. The effect of variation in TDF on food assimilation and TP was tested using three alternative TDFs reported in review papers. We then created a new method that used food source-specific TDFs (reported separately for herbivores and carnivores) weighted in proportion to estimated assimilation of resources according to mixing model estimates to estimate TP (hereafter TP_WAR). We found that plant material was not assimilated in a proportion similar to its importance in the diet of fish at a freshwater site, and the new method yielded best assimilation estimates. Animal material made greatest contributions to fish biomass irrespective of TDFs used in the mixing model. The new method produced TP estimates consistent with differences in estimated food assimilation along the salinity gradient. Our findings support the idea that food source-specific TDFs should be used in trophic studies of omnivores, since the method improved our ability to estimate trophic position and resource assimilation, two important ecological indicators.     

Are you what you eat? A highly transient and prey‐influenced gut microbiome in the grey house spider Badumna longinqua

Stable core microbial communities have been described in numerous animal species and are commonly associated with fitness benefits for their hosts. Recent research, however, highlights examples of species whose microbiota are transient and environmentally derived. Here, we test the effect of diet on gut microbial community assembly in the spider Badumna longinqua. Using 16S rRNA gene amplicon sequencing combined with quantitative PCR, we analyzed diversity and abundance of the spider's gut microbes, and simultaneously characterized its prey communities using nuclear rRNA markers. We found a clear correlation between community similarity of the spider's insect prey and gut microbial DNA, suggesting that microbiome assembly is primarily diet‐driven. This assumption is supported by a feeding experiment, in which two types of prey—crickets and fruit flies—both substantially altered microbial diversity and community similarity between spiders, but did so in different ways. After cricket consumption, numerous cricket‐derived microbes appeared in the spider's gut, resulting in a rapid homogenization of microbial communities among spiders. In contrast, few prey‐associated bacteria were detected after consumption of fruit flies; instead, the microbial community was remodelled by environmentally sourced microbes, or abundance shifts of rare taxa in the spider's gut. The reshaping of the microbiota by both prey taxa mimicked a stable core microbiome in the spiders for several weeks post feeding. Our results suggest that the spider's gut microbiome undergoes pronounced temporal fluctuations, that its assembly is dictated by the consumed prey, and that different prey taxa may remodel the microbiota in drastically different ways.     

‘Are fish what they eat’ all year round?

Isotope turnover in muscle of ectotherms depends primarily on growth rather than on metabolic replacement. Ectotherms, such as fish, have a discontinuous pattern of growth over the year, so the isotopic signature of muscle (δ¹³C and δ¹⁵N) may only reflect food consumed during periods of growth. In contrast, the liver is a regulatory tissue, with a continuous protein turnover. Therefore, the isotopic composition of liver should respond year round to changes in the isotopic signature of food sources. Therefore, we predicted that (1) Whitefish in Lake Geneva would have larger seasonal variation in the isotopic variation of the liver compared to that of the muscle tissue, and (2) the isotope composition of fish muscle would reflect a long-term image of the isotope composition of the food consumed only throughout the growth period. To test these expectations, we compared the isotope compositions of Whitefish muscle, liver and food in a 20-month study. We found that the seasonal amplitude of isotope variation was two to three times higher in liver compared to muscle tissue. During the autumn and winter, when growth was limited, only the isotopic signature of liver responded to changes in the isotope composition of the food sources. The δ¹³C and δ¹⁵N of muscle tissue only reflected the food consumed during the spring and summer growth period.     

What you need is what you eat? Prey selection by the bat Myotis daubentonii

Optimal foraging theory predicts that predators are selective when faced with abundant prey, but become less picky when prey gets sparse. Insectivorous bats in temperate regions are faced with the challenge of building up fat reserves vital for hibernation during a period of decreasing arthropod abundances. According to optimal foraging theory, prehibernating bats should adopt a less selective feeding behaviour – yet empirical studies have revealed many apparently generalized species to be composed of specialist individuals. Targeting the diet of the bat Myotis daubentonii, we used a combination of molecular techniques to test for seasonal changes in prey selectivity and individual‐level variation in prey preferences. DNA metabarcoding was used to characterize both the prey contents of bat droppings and the insect community available as prey. To test for dietary differences among M. daubentonii individuals, we used ten microsatellite loci to assign droppings to individual bats. The comparison between consumed and available prey revealed a preference for certain prey items regardless of availability. Nonbiting midges (Chironomidae) remained the most highly consumed prey at all times, despite a significant increase in the availability of black flies (Simuliidae) towards the end of the season. The bats sampled showed no evidence of individual specialization in dietary preferences. Overall, our approach offers little support for optimal foraging theory. Thus, it shows how novel combinations of genetic markers can be used to test general theory, targeting patterns at both the level of prey communities and individual predators.     

Which geometric model for the curvature of 2-D shape contours?

We investigated the geometric representations underlying the perception of 2-D contour curvature. 88 arcs representing lower and upper halves of concentric circles, or halves of ellipses derived mathematically through planar projection by affinity with the circles, a special case of Newton's transform, were generated to produce curved line segments with negative and positive curvature and varying sagitta (sag) and/or aspect ratio. Aspect ratio is defined here as the ratio between the sagitta and the chord-length of a given arc. The geometric properties of the arcs suggest a regrouping into four structural models. The 88 stimuli were presented in random order to 16 observers eight of whom were experienced in the mathematical and visual analysis of 2-D curvature ('expert observers'), and eight of whom were not ('non-expert observers'). Observers had to give a number, on a psychophysical scale from 0 to 10, that was to reflect the magnitude of curvature they perceived in a given arc. The results show that the subjective magnitude of curvature increases exponentially with the aspect ratio and linearly with the sagitta of the arcs for both experts and nonexperts. Statistical analysis of the correlation coefficients of linear fits to individual data represented on a logarithmic scale reveals significantly higher correlation coefficients for aspect ratio than for sagitta. The difference is not significant when curves with the longest chords only (7 degrees -10 degrees ) are considered. The geometric model that produces the best psychometric functions is described by a combination of arcs of vertically and horizontally oriented ellipses, indicating that perceptual sensations of 2-D contour curvature are based on geometric representations that suggest properties of 3-D structures. A 'buckled bar model' is shown to optimally account for the perceptual data of all observers with the exception of one expert. His perceptual data can be linked to a more analytical, less 'naturalistic' representation originating from a specific perceptual experience, which is discussed. It is concluded that the structural properties of 'real' objects are likely to determine even the most basic geometric representations underlying the perception of curvature in 2-D images. A specific perceptual learning experience may engender changes in such representations.     

Are more diverse parts of the mammalian skull more?labile?

Morphological variation is unevenly distributed within the mammalian skull; some of its parts have diversified more than others. It is commonly thought that this pattern of variation is mainly the result of the structural organization of the skull, as defined by the pattern and magnitude of trait covariation. Patterns of trait covariation can facilitate morphological diversification if they are aligned in the direction of selection, or these patterns can constrain diversification if oriented in a different direction. Within this theoretical framework, it is thought that more variable parts possess patterns of trait covariation that made them more capable of evolutionary change, that is, are more labile. However, differences in the degree of morphological variation among skull traits could arise despite variation in trait lability if, for example, some traits have evolved at a different rate and/or undergone stabilizing selection. Here, we test these hypotheses in the mammalian skull using 2D geometric morphometrics to quantify skull shape and estimating constraint, rates of evolution, and lability. Contrary to the expectations, more variable parts of the skull across mammalian species are less capable of evolutionary change than are less variable skull parts. Our results suggest that patterns of morphological variation in the skull could result from differences in rate of evolution and stabilizing selection.     

Why just eat in,when you can also eat out?

The current working definition of autophagy is the following: all processes in which intracellular material is degraded within the lysosome/vacuole and where the macromolecular constituents are recycled. There are several ways to classify the different types of autophagy. For example, we can separate autophagy into two primary types, based on the initial site of cargo sequestration. In particular, during microautophagy and chaperone-mediated autophagy, uptake occurs directly at the limiting membrane of the lysosome or vacuole. In contrast, macroautophagy—whether selective or nonselective—and endosomal microautophagy involve sequestration within an autophagosome or an omegasome, or late endosomes/multivesicular bodies, respectively; the key point being that in these types of autophagy the initial sequestration event does not occur at the limiting membrane of the degradative organelle. In any case, the cargo is ultimately delivered into the lysosome or vacuole lumen for subsequent degradation. Thus, I think most autophagy researchers view the degradative organelle as the ultimate destination of the pathway. Indeed, this fits with the general concept that organelles allow reactions to be compartmentalized. With regard to the lysosome or vacuole, this also confers a level of safety by keeping the lytic contents away from the remainder of the cell. If we are willing to slightly modify our definition of autophagy, with a focus on “degradation of a cell’s own components through the lysosomal/vacuolar machinery,” we can include a newly documented process, programmed nuclear destruction (PND).     

What does geometric mean,mean geometrically? Assessing the utility of geometric mean and other size variables in studies of skull allometry

This study investigated the effects of using different size variables for interpretations of relative orbit size and mandibular robusticity. Thirty-three skull measurements taken on 385 platyrrhines representing 12 of 16 New World monkey genera (in addition to body mass and total body length) were used singly and in combinations (by taking the geometric mean of all measurements) as size variables to produce relative size indices of orbit area and mandibular thickness. These indices were then compared to investigate which size variables proved effective at differentiating nocturnal from diurnal taxa and hard object from soft object feeders based upon results from previous biomechanical studies. It was found that certain groups of size variables consistently produced the a priori expectations and resulted in lower coefficients of variation. The general principles shared by these size variables were that they sampled anatomically remote regions of the skull that appear to be functionally independent from the trait being evaluated and they were nearly always geometric mean combinations composed of a relatively high number (>or=12) of large measurements. Suggestions are also presented for amending these principles for use with incomplete material such as fossils.     

Are geometric morphometric analyses replicable? Evaluating landmark measurement error and its impact on extant and fossil Microtus classification

Geometric morphometric analyses are frequently employed to quantify biological shape and shape variation. Despite the popularity of this technique, quantification of measurement error in geometric morphometric datasets and its impact on statistical results is seldom assessed in the literature. Here, we evaluate error on 2D landmark coordinate configurations of the lower first molar of five North American Microtus (vole) species. We acquired data from the same specimens several times to quantify error from four data acquisition sources: specimen presentation, imaging devices, interobserver variation, and intraobserver variation. We then evaluated the impact of those errors on linear discriminant analysis‐based classifications of the five species using recent specimens of known species affinity and fossil specimens of unknown species affinity. Results indicate that data acquisition error can be substantial, sometimes explaining >30% of the total variation among datasets. Comparisons of datasets digitized by different individuals exhibit the greatest discrepancies in landmark precision, and comparison of datasets photographed from different presentation angles yields the greatest discrepancies in species classification results. All error sources impact statistical classification to some extent. For example, no two landmark dataset replicates exhibit the same predicted group memberships of recent or fossil specimens. Our findings emphasize the need to mitigate error as much as possible during geometric morphometric data collection. Though the impact of measurement error on statistical fidelity is likely analysis‐specific, we recommend that all geometric morphometric studies standardize specimen imaging equipment, specimen presentations (if analyses are 2D), and landmark digitizers to reduce error and subsequent analytical misinterpretations.     

Are soils in urban ecosystems compacted? A citywide analysis

Soil compaction adversely influences most terrestrial ecosystem services on which humans depend. This global problem, affecting over 68 million ha of agricultural land alone, is a major driver of soil erosion, increases flood frequency and reduces groundwater recharge. Agricultural soil compaction has been intensively studied, but there are no systematic studies investigating the extent of compaction in urban ecosystems, despite the repercussions for ecosystem function. Urban areas are the fastest growing land-use type globally, and are often assumed to have highly compacted soils with compromised functionality. Here, we use bulk density (BD) measurements, taken to 14 cm depth at a citywide scale, to compare the extent of surface soil compaction between different urban greenspace classes and agricultural soils. Urban soils had a wider BD range than agricultural soils, but were significantly less compacted, with 12 per cent lower mean BD to 7 cm depth. Urban soil BD was lowest under trees and shrubs and highest under herbaceous vegetation (e.g. lawns). BD values were similar to many semi-natural habitats, particularly those underlying woody vegetation. These results establish that, across a typical UK city, urban soils were in better physical condition than agricultural soils and can contribute to ecosystem service provision.     

Did Pleistocene glaciations shape genetic patterns of European ostracods? A phylogeographic analysis of two species with asexual reproduction

Nested clade analyses (NCA) and likelihood mapping were applied to DNA sequence data of the ribosomal ITS1 and mitochondrial COI region from two non-marine ostracod species. The aim was to test whether Pleistocene glaciations may have shaped genetic and geographic patterns. According to the results from both types of analyses, evidence was lacking for any kind of geographic grouping of European (and one African) population from the putatively ancient asexual ostracod, Darwinula stevensoni. This counters the possibility that a recent selective sweep could have caused the low intraspecific, genetic diversity observed in this species. One of the most cited hypotheses to explain geographic parthenogenesis invokes faster, postglacial colonization by asexual lineages. However, no evidence for northern ‘range expansion’ of asexual haplotypes was found for Eucypris virens, a species with geographic parthenogenesis. Rather, the outcome of the NCA reveals that phylogeographic relationships are characterized by ‘restricted dispersal with isolation by (geographic) distance’. This result suggests that either no faster, postglacial range expansion of asexuals occurred in E. virens or, that patterns of subsequent colonization became ‘overwritten’ by more recent dispersal events. Likelihood mapping provides evidence for the second scenario because genetic instead of geographic clustering was statistically supported. Handling editor: K. Martens