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Synopsis The green turtle (Chelonia mydas) is a circumglobal species with a wide dietary breadth that varies among regions and life history stages. Comprehensive understanding of foraging ecology over space and time is critical to inform conservation and management of this species and its habitats. Here, we used DNA metabarcoding to test candidate primer sets with 39 gut content homogenates from stranded green turtles (FL, USA) to identify primer sets that maximize detection of food items and specificity of taxonomic classifications. We tested six existing universal primer sets to detect plants, animals, and eukaryotes more broadly (CO1, 18SV1-V3, 18SV4, rbcL, UPA, ITS). The CO1 and 18SV4 primer sets produced the greatest number of dietary amplicon sequence variants (ASVs) and unique taxonomic classifications, and they were the only primer sets to amplify taxa from all three kingdoms relevant to green turtle diet (Animalia, Chromista, and Plantae). Even though the majority of CO1-derived reads were of host origin (>90%), this primer set still produced the largest number of dietary ASVs classified to species among the six primer sets. However, because the CO1 primer set failed to detect both vascular plants and green algae, we do not recommend the use of this primer set on its own to characterize green turtle diet. Instead, our findings support previous research highlighting the utility of using multiple primer sets, specifically targeting CO1 and the V4 region of the 18S gene, as doing so will provide the most comprehensive understanding of green turtle diet. More generally, our results highlight the importance of primer and loci selection and the need to validate primer sets against the study system of interest. The addition of DNA metabarcoding with optimized primer sets to the sea turtle researcher's toolbox will both increase our understanding of foraging ecology and better inform science-based conservation and ecosystem management.

DNA metabarcoding is a molecular technique frequently used to characterize diet composition of insectivorous birds. However, results are sensitive to methodological decisions made during sample processing, with primer selection being one of the most critical. The most frequently used DNA metabarcoding primer set for avian insectivores is ZBJ. However, recent studies have found that ZBJ produces significant biases in prey classification that likely influence our understanding of foraging ecology. A new primer set, ANML, has shown promise for characterizing insectivorous bat diets with fewer taxonomic biases than ZBJ, but ANML has not yet been used to study insectivorous birds. Here, we evaluate the ANML primer set for use in metabarcoding of avian insectivore diets through comparison with the more commonly used ZBJ primer set. Fecal samples were collected from both adult and nestling Purple Martins (Progne subis subis) at 2 sites in the USA and 1 site in Canada to maximize variation in diet composition and to determine if primer selection impacts our understanding of diet variation among sites. In total, we detected 71 arthropod prey species, 39 families, and 10 orders. Of these, 40 species were uniquely detected by ANML, whereas only 11 were uniquely detected by ZBJ. We were able to classify 54.8% of exact sequence variants from ANML libraries to species compared to 33.3% from ZBJ libraries. We found that ANML outperformed ZBJ for PCR efficacy, taxonomic coverage, and specificity of classification, but that using both primer sets together produced the most comprehensive characterizations of diet composition. Significant variation in both alpha- and beta-diversity between sites was found using each primer set separately and in combination. To our knowledge, this is the first published metabarcoding study using ANML primers to describe avian diet, and also the first to directly compare results returned by ANML and ZBJ primer sets.

Identifying the composition of avian diets is a critical step in characterizing the roles of birds within ecosystems. However, because birds are a diverse taxonomic group with equally diverse dietary habits, gaining an accurate and thorough understanding of avian diet can be difficult. In addition to overcoming the inherent difficulties of studying birds, the field is advancing rapidly, and researchers are challenged with a myriad of methods to study avian diet, a task that has only become more difficult with the introduction of laboratory techniques to dietary studies. Because methodology drives inference, it is important that researchers are aware of the capabilities and limitations of each method to ensure the results of their study are interpreted correctly. However, few reviews exist which detail each of the traditional and laboratory techniques used in dietary studies, with even fewer framing these methods through a bird-specific lens. Here, we discuss the strengths and limitations of morphological prey identification, DNA-based techniques, stable isotope analysis, and the tracing of dietary biomolecules throughout food webs. We identify areas of improvement for each method, provide instances in which the combination of techniques can yield the most comprehensive findings, introduce potential avenues for combining results from each technique within a unified framework, and present recommendations for the future focus of avian dietary research.

Dietary lipid peroxides (LOOHs) have been linked to gut pathologies including inflammatory bowel disease and cancer. As poorly differentiated (PDiff) intestinal epithelial (Caco-2) cells represent tumor cells and could model intestinal crypt cells, we investigated the cellular response of PDiff Caco-2 cells to the most common dietary LOOH, 13-hydroperoxyoctadecadienoic acid (13-HPODE), using RNA sequencing (RNA-seq). Further, we compared the results with the transcriptomic profiles of PDiff cells exposed to linoleic acid (LA) or hydrogen peroxide (H2O2). The results showed that 13-HPODE treatment induces expression of genes related to detoxification and several metabolic pathways including glycogen and amino acid metabolism, which may create a tumorigenic environment despite the downregulation of some proliferation-related genes. 13-HPODE also enhanced peroxisome proliferator-activated receptor signaling involved in lipid metabolism, homeostasis, and inflammation. Additionally, results indicated that 13-HPODE impacts ribosome biogenesis, phagosome, and mitochondrial function through disrupted electron transport chain, which may contribute to disease development or progression. RNA-seq results were validated using qRT-PCR. This study provides an understanding of PDiff Caco-2 cell response to 13-HPODE and the mechanisms by which 13-HPODE modulates cellular processes that may contribute to disease development or progression.

Lipid peroxides (LOOHs) abound in processed food and have been implicated in the pathology of diverse diseases including gut, cardiovascular, and cancer diseases. Recently, RNA Sequencing (RNA-seq) has been widely used to profile gene expression. To characterize gene expression and pathway dysregulation upon exposure to peroxidized linoleic acid, we incubated intestinal epithelial cells (Caco-2) with 100 µM of 13-hydroperoxyoctadecadienoic acid (13-HPODE) or linoleic acid (LA) for 24 h. Total RNA was extracted for library preparation and Illumina HiSeq sequencing. We identified 3094 differentially expressed genes (DEGs) in 13-HPODE-treated cells and 2862 DEGs in LA-treated cells relative to untreated cells. We show that 13-HPODE enhanced lipid metabolic pathways, including steroid hormone biosynthesis, PPAR signaling, and bile secretion, which alter lipid uptake and transport. 13-HPODE and LA treatments promoted detoxification mechanisms including cytochrome-P450. Conversely, both treatments suppressed oxidative phosphorylation. We also show that both treatments may promote absorptive cell differentiation and reduce proliferation by suppressing pathways involved in the cell cycle, DNA synthesis/repair and ribosomes, and enhancing focal adhesion. A qRT-PCR analysis of representative DEGs validated the RNA-seq analysis. This study provides insights into mechanisms by which 13-HPODE alters cellular processes and its possible involvement in mitochondrial dysfunction-related disorders and proposes potential therapeutic strategies to treat LOOH-related pathologies.

Nasal carriage of Staphylococcus aureus is a risk factor for infection, but it is not yet understood why some individuals carry nasal S. aureus persistently, intermittently, or seemingly not at all when tested via culture methods. This study compared the nasal microbiomes of established S. aureus carriers and noncarriers, identified species associated with noncarriage, and tested them for anti-S. aureus activity using assays developed to model the nutrient-limited nasal mucosa., Staphylococcus aureus nasal carriage provides the bacterial reservoir for opportunistic infection. In comparing the nasal microbiomes of culture-defined persistent S. aureus carriers versus noncarriers, we detected S. aureus DNA in all noses, including those with an established history of S. aureus negativity based on culture. Colonization with Gammaproteobacteria, including Klebsiella aerogenes, Citrobacter koseri, Moraxella lincolnii, and select Acinetobacter spp., was associated with S. aureus noncarriage. We next developed physiological competition assays for testing anti-S. aureus activity of isolated nasal species, utilizing medium modeling the nutrient-limited fluid of the nasal mucosa, polarized primary nasal epithelia, and nasal secretions. K. aerogenes from the nose of an S. aureus noncarrier demonstrated >99% inhibition of S. aureus recovery in all assays, even when S. aureus was coincubated in 9-fold excess. Secreted S. aureus inhibitory proteins from K. aerogenes and M. lincolnii were heat-stable and

Identifying the adverse impacts of pesticide exposure in rice ecosystems is essential to guide regulations that are protective of wildlife and human health. Amphibians are valuable indicators within rice ecosystems because pesticide applications coincide with sensitive reproductive and developmental life stages. We conducted two experiments using wild cane toads (Rhinella marina) to test 1) whether environmentally relevant exposure to a commercial formulation of butachlor, an acetanilide herbicide used extensively in rice, affects amphibian development and 2) whether cane toad tadpoles are capable of acclimatizing to sub-lethal exposure. First, we exposed wild cane toads to 0.002, 0.02, or 0.2 mg/L of butachlor (Machete EC), during distinct development stages (as eggs and hatchlings, as tadpoles, or continuously) for 12 days. Next, we exposed a subset of animals from the first experiment to a second, lethal concentration and examined survivorship. We found that cane toads exposed to butachlor developed slower and weighed less than controls, and that development of the thyroid gland was affected: exposed individuals had smaller thyroid glands and thyrocyte cells, and more individual follicles. Analyses of the transcriptome revealed that butachlor exposure resulted in downregulation of transcripts related to metabolic processes, anatomic structure development, immune system function, and response to stress. Last, we observed evidence of acclimatization, where animals exposed to butachlor early in life performed better than naive animals during a second exposure. Our findings indicate that the commercial formulation of butachlor, Machete EC, causes thyroid endocrine disruption in vertebrates, and suggest that exposure in lowland irrigated rice fields presents a concern for wildlife and human health. Furthermore, we establish that developmental assays with cane toads can be used to screen for adverse effects of pesticides in rice fields.

Animals must balance various costs and benefits when deciding when to breed. The costs and benefits of breeding at different times have received much attention, but most studies have been limited to investigating short-term season-to-season fitness effects. However, breeding early, versus late, in a season may influence lifetime fitness over many years, trading off in complex ways across the breeder’s lifespan. In this study, we examined the complete life histories of 867 female tree swallows (Tachycineta bicolor) breeding in Ithaca, New York, between 2002 and 2016. Earlier breeders outperformed later breeders in short-term measures of reproductive output and offspring quality. Though there were weak indications that females paid long-term future survival costs for breeding early, lifetime fledgling output was markedly higher overall in early-breeding birds. Importantly, older females breeding later in the season did not experience compensating life history advantages that suggested an alternative equal-fitness breeding strategy. Rather, most or all of the swallows appear to be breeding as early as they can, and differences in lay dates appear to be determined primarily by differences in individual quality or condition. Lay date had a significant repeatability across breeding attempts by the same female, and the first lay date of females fledged in our population was strongly influenced by the first lay date of their mothers, indicating the potential for ongoing selection on lay date. By examining performance over the entire lifespan of a large number of individuals, we were able to clarify the relationship between timing of breeding and fitness and gain new insight into the sources of variability in this important life history trait.

Despite keen interest in extra-pair mating in birds, its adaptive significance remains unresolved. Here, we use a multi-year dataset to test whether traits of a female's social mate influence her propensity to produce extra-pair offspring in a population of house wrens, and whether producing extra-pair young has consequences for a female's fitness through effects on offspring survival. Females were most likely to produce extra-pair offspring when paired with old males and when paired with males on poor-quality territories, although this latter effect was marginally nonsignificant. Among offspring, the cutaneous immunity of within-pair young decreased as the age of their sires increased, but cutaneous immunity of extra-pair young was not affected by the age of their extra-pair sires or by the age of the males rearing them. Extra-pair offspring were more likely than within-pair offspring to return as breeding adults to the local population, with extra-pair sons being more likely to return as a breeder for multiple years. Our findings support the hypothesis that females produce extra-pair offspring to enhance their inclusive fitness beyond what they are capable of given the male with which they are socially paired.

We report here the draft genome sequence of a novel Xenophilus species cultured from the skin of a southern leopard frog ( Rana sphenocephala ). Compared to previously sequenced bacterial genomes, our novel isolate showed the most significant homology with Xenophilus azovorans . The assembled genome is 3,978,285 bp, with 3,704 predicted genes and one predicted plasmid.

Measures of body condition, immune function, and hematological health are widely used in ecological studies of vertebrate populations, predicated on the assumption that these traits are linked to fitness. However, compelling evidence that these traits actually predict long-term survival and reproductive success among individuals in the wild is lacking. Here, we show that body condition (i.e., size-adjusted body mass) and cutaneous immune responsiveness to phytohaemagglutinin (PHA) injection among neonates positively predict recruitment and subsequent longevity in a wild, migratory population of house wrens (Troglodytes aedon). However, neonates with intermediate hematocrit had the highest recruitment and longevity. Neonates with the highest PHA responsiveness and intermediate hematocrit prior to independence eventually produced the most offspring during their lifetime breeding on the study site. Importantly, the effects of PHA responsiveness and hematocrit were revealed while controlling for variation in body condition, sex, and environmental variation. Thus, our data demonstrate that body condition, cutaneous immune responsiveness, and hematocrit as a neonate are associated with individual fitness. Although hematocrit's effect is more complex than traditionally thought, our results suggest a previously underappreciated role for this trait in influencing survival in the wild.

Adult male and female birds typically respond differently to immunological challenges, but whether this difference is present in altricial nestlings is not well-documented. Furthermore, the timing of the development of different axes of the immune system might vary in nestlings and also be affected by differences in condition and health state. We tested for sex-related differences in the immune response of nestling House Wrens (Troglodytes aedon Vieillot, 1809) to the injection of phytohaemagglutinin (PHA) and in the bacteria-killing capacity of their plasma. Based on prior work, we predicted that if there were sex-related differences in immune responsiveness, they would most likely occur when the sexes differed in some measure of condition or health state. Female nestlings had a stronger response to the injection of PHA than males in the one of three breeding seasons in which the condition of nestling females exceeded that of males, suggesting that the response to PHA injection is condition-dependent rather than sex-dependent. The sexes, however, did not differ in bactericidal activity, suggesting that different axes of the immune system may not be affected to the same degree by differences in sex or in condition.

Immunological measures are increasingly being applied to ecological and evolutionary studies of wild vertebrates, yet frequently it is not clear how condition and environmental factors correlate with various immune parameters. We used mixed-model ANOVA to examine the effects of several measures of condition (both morphological and physiological) and environmental factors on two measures of immune responsiveness in nestling house wrens (Troglodytes aedon L.) to test the hypothesis that nestlings in good condition mount stronger immune responses than those in poor condition. Based on previous studies, we predicted that the innate bactericidal response would be less likely to be affected by condition-related factors than the cutaneous response, which includes both innate and the more costly adaptive components. Both cutaneous immune activity (i.e., phytohaemagglutinin [PHA] response) and innate immune responsiveness (i.e., plasma bactericidal activity) varied significantly among broods. Nestling PHA response was significantly influenced by year, mass, and the time of day that the challenge was administered. However, besides nest of origin, no other variable examined had a significant effect on bactericidal activity. Morphological condition, assessed as body mass adjusted for structural size, differed significantly among nests and years and was positively correlated with hematocrit but not plasma albumin/gamma-globulin proteins, indicating that these are measures of different aspects of health state.

Background Life-history studies of wild bird populations often focus on the relationship between an individual’s condition and its capacity to mount an immune response, as measured by a commonly-employed assay of cutaneous immunity, the PHA skin test. In addition, haematocrit, the packed cell volume in relation to total blood volume, is often measured as an indicator of physiological performance. A multi-year study of a wild population of house wrens has recently revealed that those exhibiting the highest condition and strongest PHA responses as nestlings are most likely to be recruited to the breeding population and to breed through two years of age; in contrast, intermediate haematocrit values result in the highest recruitment to the population. Selection theory would predict, therefore, that most of the underlying genetic variation in these traits should be exhausted resulting in low heritability, although such traits may also exhibit low heritability because of increased residual variance. Here, we examine the genetic and environmental variation in condition, cutaneous immunity, and haematocrit using an animal model based on a pedigree of approximately 2,800 house wrens. Results Environmental effects played a paramount role in shaping the expression of the fitness-related traits measured in this wild population, but two of them, condition and haematocrit, retained significant heritable variation. Condition was also positively correlated with both the PHA response and haematocrit, but in the absence of any significant genetic correlations, it appears that this covariance arises through parallel effects of the environment acting on this suite of traits. Conclusions The maintenance of genetic variation in different measures of condition appears to be a pervasive feature of wild bird populations, in contradiction of conventional selection theory. A major challenge in future studies will be to explain how such variation persists in the face of the directional selection acting on condition in house wrens and other species.

House wrens are typically socially monogamous, but frequently engage in extra-pair matings leading to multisired broods. Because females do not appear to acquire direct material benefits from their extra-pair mates, we tested the hypothesis that female house wrens derive indirect genetic benefits, such as enhanced immunocompetence (cutaneous immune activity, humoral immunity, and plasma bactericidal activity) and condition (size and haematoserological traits) for their offspring, by mating polyandrously. We predicted that extra-pair young (EPY) should show greater immune responsiveness and better body condition than their within-pair maternal half-siblings (WPY). Contrary to our prediction, WPY had higher cutaneous immune activity than their EPY brood-mates in two of three years, and EPY and WPY did not differ in measures of innate and humoral immunity. WPY also had higher albumin to gamma-globulin ratios than EPY; however, they were not in better condition based on other measures. EPY had consistently longer tarsi (a measure of long-bone size) than their WPY half-siblings, suggesting that females engage in extra-pair copulations with larger males. The benefits of large structural size in the study population is unknown, but based on evidence from other passerines, we suggest that structural size may be an important fitness-related trait in house wrens. We conclude that our results are not consistent with the hypothesis that females gain immune-related benefits for their offspring by engaging in extra-pair matings. Further study of the fitness consequences of differences in tarsus length is needed to determine whether females acquire size-related benefits for their offspring from extra-pair mates.

Single components of the immune system are widely used to assess immune function in free-living vertebrates. However, as different immunological components are triggered by different types of threats and may be regulated independently, there is little reason to assume that they should respond similarly if challenged. We investigated whether three commonly assayed immune responses, cutaneous immune activity (phytohaemagglutinin assay), antibody response (tetanus toxoid immunization), and plasma bactericidal activity (Escherichia coli killing) are positively related in nestling house wrens (Troglodytes aedon). Multivariate analysis revealed significant differences in overall immune responsiveness among broods (i.e. nests), primarily attributable to differences in plasma bactericidal activity. Among broods, humoral immune response was negatively related to cutaneous immune activity and positively related to plasma bactericidal activity. We found no significant relationships among these measures of immunity among individual nestlings within broods. Our results suggest that different broods (i.e. families) invest differentially in the various branches of the immune system. Further study is needed to characterize the roles of maternal, genetic and environmental effects on the expression of this physiological bias.