Changes in digestive traits and body nutritional composition accommodate a trophic niche shift in Trinidadian guppies

SEED: A framework for integrating ecological stoichiometry and eco-evolutionary dynamics

Characterising the extent and sources of intraspecific variation and their ecological consequences is a central challenge in the study of eco-evolutionary dynamics. Ecological stoichiometry, which uses elemental variation of organisms and their environment to understand ecosystem patterns and processes, can be a powerful framework for characterising eco-evolutionary dynamics. However, the current emphasis on the relative content of elements in the body (i.e. organismal stoichiometry) has constrained its application. Intraspecific variation in the rates at which elements are acquired, assimilated, allocated or lost is often greater than the variation in organismal stoichiometry. There is much to gain from studying these traits together as components of an 'elemental phenotype'. Furthermore, each of these traits can have distinct ecological effects that are underappreciated in the current literature. We propose a conceptual framework that explores how microevolutionary change in the elemental phenotype occurs, how its components interact with each other and with other traits, and how its changes can affect a wide range of ecological processes. We demonstrate how the framework can be used to generate novel hypotheses and outline pathways for future research that enhance our ability to explain, analyse and predict eco-evolutionary dynamics.

Shifts in gut microbiome across five decades of repeated guppy translocations in Trinidadian streams

An organism's gut microbiome can alter its fitness, yet we do not know how gut microbiomes change as their hosts evolve in the wild. We took advantage of a five-decade 'chronosequence' of translocated fish populations to examine associated changes in the gut microbiome. Populations of Trinidadian guppies have displayed parallel phenotypic convergence six times when moved from high predation (HP) to low predation (LP) environments. Across four drainages, we found microbiomes of fish translocated 5-6 years prior to sampling were already distinct from the microbiomes of their HP source populations. Changes in environmental conditions were most important in driving this shift, followed by phenotypic shifts in gut morphology. After 30-60 years in LP environments, microbiome composition was still distinct from native LP populations, but microbiome function was not. We found some evidence that nitrogen fixation enhanced gut nutrient absorption, but most functional shifts were not parallel across drainages. Stream-and drainage-specific signatures were present for both composition and function, despite our overall finding of consistent microbiome change across drainages. As we unravel the complexities of host-microbiome evolution in the wild, studies should consider environmental microbial colonization, host phenotypic plasticity in nature, and more realistic environmental conditions excluded from laboratory studies.

Comparative transcriptomics reveal tissue level specialization towards diet in prickleback fishes

Beyond a few obvious examples (e.g., gut length, amylase activity), digestive and metabolic specializations towards diet remain elusive in fishes. Thus, we compared gut length, δ¹³C and δ¹⁵N signatures of the liver, and expressed genes in the intestine and liver of wild-caught individuals of four closely-related, sympatric prickleback species (family Stichaeidae) with different diets: Xiphister mucosus (herbivore), its sister taxon X. atropurpureus (omnivore), Phytichthys chirus (omnivore) and the carnivorous Anoplarchus purpurescens. We also measured the same parameters after feeding them carnivore or omnivore diets in the laboratory for 4 weeks. Growth and isotopic signatures showed assimilation of the laboratory diets, and gut length was significantly longer in X. mucosus in comparison to the other fishes, whether in the wild, or in the lab consuming the different diets. Dozens of genes relating to digestion and metabolism were observed to be under selection in the various species, but P. chirus stood out with some genes in the liver showing strong positive selection, and these genes correlating with differing isotopic incorporation of the laboratory carnivore diet in this species. Although the intestine showed variation in the expression of hundreds of genes in response to the laboratory diets, the liver exhibited species-specific gene expression patterns that changed very little (generally <40 genes changing expression, with P. chirus providing an exception). Overall, our results suggest that the intestine is plastic in function, but the liver may be where specialization manifests since this tissue shows species-specific gene expression patterns that match with natural diet.

Consumer trait responses track change in resource supply along replicated thermal gradients

Rising temperatures may alter consumer diets through increased metabolic demand and altered resource availability. However, current theories assessing dietary shifts with warming do not account for a change in resource availability. It is unknown whether consumers will increase consumption rates or consume different resources to meet increased energy requirements and whether the dietary change will lead to associated variation in morphology and nutrient utilization. Here, we used populations of Gambusia affinis across parallel thermal gradients in New Zealand (NZ) and California (CA) to understand the influence of temperature on diets, morphology and stoichiometric phenotypes. Our results show that with increasing temperature in NZ, mosquitofish consumed more plant material, whereas in CA mosquitofish shifted towards increased consumption of invertebrate prey. In both regions, populations with plant-based diets had fuller guts, longer relative gut lengths, better-orientated mouths and reduced body elemental %C and N/P. Together, our results show multiple pathways by which consumers may alter their feeding patterns with rising temperatures, and they suggest that warming-induced changes to resource availability may be the principal determinant of which pathway is taken.

Understanding Nutrition and Metabolism of Threatened, Data-Poor Rheophilic Fishes in Context of Riverine Stocking Success- Barbel as a Model for Major European Drainages?

Large-bodied, river-migrating, rheophilic fishes (cyprinids) such as barbel Barbus barbus, nase Chondrostoma nasus, asp Leuciscus aspius, and vimba bream Vimba vimba are threatened in major European drainages. This represents the subject of our present study. Their hatchery nutrition prior to river-release is mostly on a hit-and-trial or carp-based diet basis. The study demonstrates an alternative approach to decide optimum nutrition for these conservation-priority and nutritionally data-poor fishes. The study revealed barbel as a central representative species in terms of wild body composition among other native rheophilic cyprinids considered (asp, nase, vimba bream). Taking barbel as a model, the study shows that barbel or rheophilic cyprinids may have carnivorous-like metabolism and higher requirements of S-containing, aromatic, branched-chain amino acids (AAs) than carps. Besides, there are important interactions of AAs and fatty acids (FAs) biosynthesis to consider. Only proper feeding of nutritionally well-selected diets may contribute to river stocking mandates such as steepest growth trajectory (≈less time in captivity), ideal size-at-release, body fitness (≈blend-in with wild conspecifics, predator refuge), better gastrointestinal condition, maximized body reserves of functional nutrients, and retention efficiencies (≈uncompromised physiology). Considering important physiological functions and how AA-FA interactions shape them, hatchery-raised fishes on casually chosen diets may have high chances of physiological, morphological, and behavioral deficits (≈low post-stocking survivability). Based on the observations, optimum nutrient requirements of juvenile (0+ to 1+ age) barbels are suggested. Future efforts may consider barbels as a nutrition model for conservation aquaculture of threatened and data poor rheophilic cyprinids of the region.

Extreme environmental conditions reduce coral reef fish biodiversity and productivity

Tropical ectotherms are hypothesized to be vulnerable to environmental changes, but cascading effects of organismal tolerances on the assembly and functioning of reef fish communities are largely unknown. Here, we examine differences in organismal traits, assemblage structure, and productivity of cryptobenthic reef fishes between the world’s hottest, most extreme coral reefs in the southern Arabian Gulf and the nearby, but more environmentally benign, Gulf of Oman. We show that assemblages in the Arabian Gulf are half as diverse and less than 25% as abundant as in the Gulf of Oman, despite comparable benthic composition and live coral cover. This pattern appears to be driven by energetic deficiencies caused by responses to environmental extremes and distinct prey resource availability rather than absolute thermal tolerances. As a consequence, production, transfer, and replenishment of biomass through cryptobenthic fish assemblages is greatly reduced on Earth’s hottest coral reefs. Extreme environmental conditions, as predicted for the end of the 21st century, could thus disrupt the community structure and productivity of a critical functional group, independent of live coral loss.

Brandl, Johansen et al. compare organismal traits, community structure, and productivity dynamics of cryptobenthic reef fishes across two locations, the Arabian Gulf and the Gulf of Oman, the former of which harbors the world’s hottest coral reefs. They show that environmental extremes in the Arabian Gulf result in dramatically less diverse, abundant, and productive cryptobenthic fish assemblages, which could foreshadow the future of coral reef biodiversity and functioning.

Microbiota Landscape of Gut System of Guppy Fish (Poecilia reticulata) Plays an Outstanding Role in Adaptation Mechanisms

Microbial consortium that is present in fish gut systems works together to achieve unknown specific roles. Here, we collected guppy fish from hydrocarbon- and trace metal-contaminated wastewater to assess the relationships between gut microbiota and host fish adaptation. Targeted genes and 16S rRNA amplicon sequencing have been used to identify gut bacteria of guppies. Mineral-conditioned medium contributes to identify bacteria with the ability to grow and/or to tolerate hydrocarbon and trace metals. Additionally, trace metals' tolerance minimum inhibitory concentration (MIC) of microbiota was evaluated. We first isolated bacteria from the gut system, and we showed that Bacillus spp., Staphylococcus spp., Shigella spp., Salmonella spp, Pseudomonas spp., Citrobacter spp., Salmonella enterica ssp.arizonae sp., Enterobacter spp, and Acinetobacter spp. are part of guppy gut microbiota. Some representative species are able to degrade and/or tolerate gasoline and/or diesel fuel hydrocarbons. Tolerance to trace metals was observed in Gram-positive and Gram-negative bacteria. We showed that minimal inhibitory concentration (MIC) of some microbiota isolated from gut systems has been found including for mercury (Hg) between 2 and 4‰, cobalt (Co) Co (2 and 5‰), zinc (Zn) (9 and 18‰), and plomb (Pb) (22 and 27‰). Zn and Pb were the trace metals for which the rate of tolerance was significantly higher. Finally, we showed that cytochrome c oxidase is not interfering in presence of trace metals. The working consortium showed that bacteria should work together to achieve their best.

The Expensive-Tissue Hypothesis in Vertebrates: Gut Microbiota Effect, a Review

The gut microbiota is integral to an organism’s digestive structure and has been shown to play an important role in producing substrates for gluconeogenesis and energy production, vasodilator, and gut motility. Numerous studies have demonstrated that variation in diet types is associated with the abundance and diversity of the gut microbiota, a relationship that plays a significant role in nutrient absorption and affects gut size. The Expensive-Tissue Hypothesis states (ETH) that the metabolic requirement of relatively large brains is offset by a corresponding reduction of the other tissues, such as gut size. However, how the trade-off between gut size and brain size in vertebrates is associated with the gut microbiota through metabolic requirements still remains unexplored. Here, we review research relating to and discuss the potential influence of gut microbiota on the ETH.

Effects of predation stress and food ration on perch gut microbiota

BACKGROUND

Gut microbiota provide functions of importance to influence hosts' food digestion, metabolism, and protection against pathogens. Factors that affect the composition and functions of gut microbial communities are well studied in humans and other animals; however, we have limited knowledge of how natural food web factors such as stress from predators and food resource rations could affect hosts' gut microbiota and how it interacts with host sex. In this study, we designed a two-factorial experiment exposing perch (Perca fluviatilis) to a predator (pike, Esox lucius), and different food ratios, to examine the compositional and functional changes of perch gut microbiota based on 16S rRNA amplicon sequencing. We also investigated if those changes are host sex dependent.

RESULTS

We showed that overall gut microbiota composition among individual perch significantly responded to food ration and predator presence. We found that species richness decreased with predator presence, and we identified 23 taxa from a diverse set of phyla that were over-represented when a predator was present. For example, Fusobacteria increased both at the lowest food ration and at predation stress conditions, suggesting that Fusobacteria are favored by stressful situations for the host. In concordance, both food ration and predation stress seemed to influence the metabolic repertoire of the gut microbiota, such as biosynthesis of other secondary metabolites, metabolism of cofactors, and vitamins. In addition, the identified interaction between food ration and sex emphasizes sex-specific responses to diet quantity in gut microbiota.

CONCLUSIONS

Collectively, our findings emphasize an alternative state in gut microbiota with responses to changes in natural food webs depending on host sex. The obtained knowledge from this study provided us with an important perspective on gut microbiota in a food web context.

The influence of dietary and whole-body nutrient content on the excretion of a vertebrate consumer

In many contexts, nutrient excretion by consumers can impact ecosystems by altering the availability of limiting nutrients. Variation in nutrient excretion can be predicted by mass balance models, most of which are premised on two key ideas: (1) consumers maintain fixed whole-body nutrient content (i.e., %N and %P), so-called fixed homeostasis; (2) if dietary nutrients are not matched to whole-body nutrients, excesses of any nutrient are released as excretion to maintain fixed homeostasis. Mass balance models thus predict that consumer excretion should be positively correlated with diet nutrients and negatively correlated with whole-body nutrients. Recent meta-analyses and field studies, however, have often failed to find these expected patterns, potentially because of a confounding influence—flexibility in whole-body nutrient content with diet quality (flexible homeostasis). Here, we explore the impact of flexible homeostasis on nutrient excretion by comparing the N and P excretion of four genetically diverged Trinidadian guppy (Poecilia reticulata) populations when reared on diets of variable P content. As predicted by mass balance, P excretion increased on the high-P diet, but, contrary to the notion of fixed homeostasis, guppy whole-body %P also increased on the high-P diet. While there was no overall correlation between excretion nutrients and whole-body nutrients, when the effect of diet on both whole-body and excretion nutrients was included, we detected the expected negative correlation between whole-body N:P and excretion N:P. This last result suggests that mass balance can predict excretion rates within species, but only if dietary effects on whole-body nutrient content are controlled. Flexible homeostasis can obscure patterns predicted by mass balance, creating an imperative to accurately capture an organism’s diet quality in predicting its excretion rate.

Population variation in the trophic niche of the Trinidadian guppy from different predation regimes

Population variation in trophic niche is widespread among organisms and is of increasing interest given its role in both speciation and adaptation to changing environments. Trinidadian guppies (Poecilia reticulata) inhabiting stream reaches with different predation regimes have rapidly evolved divergent life history traits. Here, we investigated the effects of both predation and resource availability on guppy trophic niches by evaluating their gut contents, resource standing stocks, and δ15N and δ13C stable isotopes across five streams during the wet season. We found that guppies from low predation (LP) sites had a consistently higher trophic position and proportion of invertebrates in their guts and assimilate less epilithon than guppies from high predation (HP) sites. Higher trophic position was also associated with lower benthic invertebrate availability. Our results suggest that LP guppies could be more efficient invertebrate consumers, possibly as an evolutionary response to greater intraspecific competition for higher quality food. This may be intensified by seasonality, as wet season conditions can alter resource availability, feeding rates, and the intensity of intraspecific competition. Understanding how guppy diets vary among communities is critical to elucidating the role of niche shifts in mediating the link between environmental change and the evolution of life histories.

Stoichiometric traits of stickleback: Effects of genetic background, rearing environment, and ontogeny

Phenotypes can both evolve in response to, and affect, ecosystem change, but few examples of diverging ecosystem‐effect traits have been investigated. Bony armor traits of fish are good candidates for this because they evolve rapidly in some freshwater fish populations, and bone is phosphorus rich and likely to affect nutrient recycling in aquatic ecosystems. Here, we explore how ontogeny, rearing environment, and bone allocation among body parts affect the stoichiometric phenotype (i.e., stoichiometric composition of bodies and excretion) of threespine stickleback. We use two populations from distinct freshwater lineages with contrasting lateral plating phenotypes (full vs. low plating) and their hybrids, which are mostly fully plated. We found that ontogeny, rearing environment, and body condition were the most important predictors of organismal stoichiometry. Although elemental composition was similar between both populations and their hybrids, we found significant divergence in phosphorus allocation among body parts and in phosphorus excretion rates. Overall, body armor differences did not explain variation in whole body phosphorus, phosphorus allocation, or phosphorus excretion. Evolutionary divergence between these lineages in both allocation and excretion is likely to have important direct consequences for ecosystems, but may be mediated by evolution of multiple morphological or physiological traits beyond plating phenotype.

The effect of top-predator presence and phenotype on aquatic microbial communities

The presence of predators can impact a variety of organisms within the ecosystem, including microorganisms. Because the effects of fish predators and their phenotypic differences on microbial communities have not received much attention, we tested how the presence/absence, genotype, and plasticity of the predatory three‐spine stickleback (Gasterosteus aculeatus) influence aquatic microbes in outdoor mesocosms. We reared lake and stream stickleback genotypes on contrasting food resources to adulthood, and then added them to aquatic mesocosm ecosystems to assess their impact on the planktonic bacterial community. We also investigated whether the effects of fish persisted following the removal of adults, and the subsequent addition of a homogenous juvenile fish population. The presence of adult stickleback increased the number of bacterial OTUs and altered the size structure of the microbial community, whereas their phenotype affected bacterial community composition. Some of these effects were detectable after adult fish were removed from the mesocosms, and after juvenile fish were placed in the tanks, most of these effects disappeared. Our results suggest that fish can have strong short‐term effects on microbial communities that are partially mediated by phenotypic variation of fish.

Increased juvenile predation is not associated with evolved differences in adult brain size in Trinidadian killifish (Rivulus hartii)

Vertebrates exhibit extensive variation in brain size. The long-standing assumption is that this variation is driven by ecologically mediated selection. Recent work has shown that an increase in predator-induced mortality is associated with evolved increases and decreases in brain size. Thus, the manner in which predators induce shifts in brain size remains unclear. Increased predation early in life is a key driver of many adult traits, including life-history and behavioral traits. Such results foreshadow a connection between age-specific mortality and selection on adult brain size. Trinidadian killifish, Rivulus hartii, are found in sites with and without guppies, Poecilia reticulata. The densities of Rivulus drop dramatically in sites with guppies because guppies prey upon juvenile Rivulus. Previous work has shown that guppy predation is associated with the evolution of adult life-history traits in Rivulus. In this study, we compared second-generation laboratory-born Rivulus from sites with and without guppies for differences in brain size and associated trade-offs between brain size and other components of fitness. Despite the large amount of existing research on the importance of early-life events on the evolution of adult traits, and the role of predation on both behavior and brain size, we did not find an association between the presence of guppies and evolutionary shifts in Rivulus brain size. Such results argue that increased rates of juvenile mortality may not alter selection on adult brain size.

Predator-driven brain size evolution in natural populations of Trinidadian killifish (Rivulus hartii)

Vertebrates exhibit extensive variation in relative brain size. It has long been assumed that this variation is the product of ecologically driven natural selection. Yet, despite more than 100 years of research, the ecological conditions that select for changes in brain size are unclear. Recent laboratory selection experiments showed that selection for larger brains is associated with increased survival in risky environments. Such results lead to the prediction that increased predation should favour increased brain size. Work on natural populations, however, foreshadows the opposite trajectory of evolution; increased predation favours increased boldness, slower learning, and may thereby select for a smaller brain. We tested the influence of predator-induced mortality on brain size evolution by quantifying brain size variation in a Trinidadian killifish, Rivulus hartii, from communities that differ in predation intensity. We observed strong genetic differences in male (but not female) brain size between fish communities; second generation laboratory-reared males from sites with predators exhibited smaller brains than Rivulus from sites in which they are the only fish present. Such trends oppose the results of recent laboratory selection experiments and are not explained by trade-offs with other components of fitness. Our results suggest that increased male brain size is favoured in less risky environments because of the fitness benefits associated with faster rates of learning and problem-solving behaviour.

The effect of brain size evolution on feeding propensity, digestive efficiency, and juvenile growth

One key hypothesis in the study of brain size evolution is the expensive tissue hypothesis; the idea that increased investment into the brain should be compensated by decreased investment into other costly organs, for instance the gut. Although the hypothesis is supported by both comparative and experimental evidence, little is known about the potential changes in energetic requirements or digestive traits following such evolutionary shifts in brain and gut size. Organisms may meet the greater metabolic requirements of larger brains despite smaller guts via increased food intake or better digestion. But increased investment in the brain may also hamper somatic growth. To test these hypotheses we here used guppy (Poecilia reticulata) brain size selection lines with a pronounced negative association between brain and gut size and investigated feeding propensity, digestive efficiency (DE), and juvenile growth rate. We did not find any difference in feeding propensity or DE between large- and small-brained individuals. Instead, we found that large-brained females had slower growth during the first 10 weeks after birth. Our study provides experimental support that investment into larger brains at the expense of gut tissue carries costs that are not necessarily compensated by a more efficient digestive system.

Contrasting Population and Diet Influences on Gut Length of an Omnivorous Tropical Fish, the Trinidadian Guppy (Poecilia reticulata)

Phenotypic plasticity is advantageous for organisms that live in variable environments. The digestive system is particularly plastic, responding to changes in diet. Gut length is the result of a trade-off between maximum nutrient absorption and minimum cost for its maintenance and it can be influenced by diet and by evolutionary history. We assessed variation in gut length of Trinidadian guppies (Poecilia reticulata) as a function of diet, season, ontogeny, and local adaptation. Populations of guppies adapted to different predation levels have evolved different life history traits and have different diets. We sampled guppies from sites with low (LP) and high predation (HP) pressure in the Aripo and Guanapo Rivers in Trinidad. We collected fish during both the dry and wet season and assessed their diet and gut length. During the dry season, guppies from HP sites fed mostly on invertebrates, while guppies in the LP sites fed mainly on detritus. During the wet season, the diet of LP and HP populations became very similar. We did not find strong evidence of an ontogenetic diet shift. Gut length was negatively correlated with the proportion of invertebrates in diet across fish from all sites, supporting the hypothesis that guppy digestive systems adapt in length to changes in diet. Population of origin also had an effect on gut length, as HP and LP fish maintained different gut lengths even in the wet season, when their diets were very similar and individuals in both types of populations fed mostly on detritus. Thus, both environment and population of origin influenced guppies gut length, but population of origin seemed to have a stronger effect. Our study also showed that, even in omnivorous fish, gut length adapted to different diets, being more evident when the magnitude of difference between animal and plant material in the diet was very large.

Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies

Diverse microbial consortia profoundly influence animal biology, necessitating an understanding of microbiome variation in studies of animal adaptation. Yet, little is known about such variability among fish, in spite of their importance in aquatic ecosystems. The Trinidadian guppy, Poecilia reticulata, is an intriguing candidate to test microbiome-related hypotheses on the drivers and consequences of animal adaptation, given the recent parallel origins of a similar ecotype across streams. To assess the relationships between the microbiome and host adaptation, we used 16S rRNA amplicon sequencing to characterize gut bacteria of two guppy ecotypes with known divergence in diet, life history, physiology and morphology collected from low-predation (LP) and high-predation (HP) habitats in four Trinidadian streams. Guts were populated by several recurring, core bacteria that are related to other fish associates and rarely detected in the environment. Although gut communities of lab-reared guppies differed from those in the wild, microbiome divergence between ecotypes from the same stream was evident under identical rearing conditions, suggesting host genetic divergence can affect associations with gut bacteria. In the field, gut communities varied over time, across streams and between ecotypes in a stream-specific manner. This latter finding, along with PICRUSt predictions of metagenome function, argues against strong parallelism of the gut microbiome in association with LP ecotype evolution. Thus, bacteria cannot be invoked in facilitating the heightened reliance of LP guppies on lower-quality diets. We argue that the macroevolutionary microbiome convergence seen across animals with similar diets may be a signature of secondary microbial shifts arising some time after host-driven adaptation.

Ontogenetic variation in the body stoichiometry of two fish species

One of the central questions of ecological stoichiometry theory is to what extent animal species maintain constant elemental composition in their bodies. Although several recent studies demonstrate intraspecific variation in animal elemental composition, relatively little is known about ontogenetic changes in vertebrates, especially during early life stages. We studied the intraspecific and interspecific ontogenetic variation in the body stoichiometry of two fish species in two different orders; fathead minnow (Pimephales promelas) and sheepshead minnow (Cyprinodon variegatus), reared under controlled laboratory conditions. During ontogeny, we measured the chemical composition of fish bodies, including carbon (C), nitrogen (N), phosphorus (P), calcium (Ca), and ribonucleic acid (RNA) contents. We found that N and RNA contents were relatively high in early life stages and declined substantially during development. In contrast, body C and C:N ratios were relatively low in embryos, post-embryos and larvae, and increased remarkably thereafter. Concentrations and ratios of some elements (e.g., Ca, P, Ca:P) did not exhibit consistent ontogenetic trends, but fluctuated dynamically between consecutive developmental stages in both species. Specific growth rates correlated significantly with RNA contents in both species. Analyses of the relative importance of different P pools at each developmental stage revealed that RNA was a considerable P pool in post-embryos, while bone-associated P was the dominant body P pool in later stages. Our results suggest that the elemental composition of fish bodies changes considerably during ontogeny. Each ontogenetic stage has its own stoichiometric signature, but the timing, magnitude and direction of ontogenetic changes can vary substantially between taxa.