Do mammals, birds, reptiles and fish have similar nitrogen conserving systems?

Archaeal diversity in the microbiomes of four wild bird species

Archaea are generally low-abundance members of the vertebrate microbiota that require specific PCR primers to be detected in metabarcoding studies, and the robust intraspecific sample size is necessary for well-supported conclusions about archaeal diversity. Using 16S rRNA gene amplicons generated using both Archaea-Specific and Universal primers, we investigated prokaryotic diversity in 110 fecal samples from four wild bird species from four different orders: Anna's Hummingbird (Calypte anna), Saltmarsh Sparrow (Ammospiza caudacuta), Ruddy Turnstone (Arenaria interpres), and Canada Goose (Branta canadensis). Our aim was to test the hypotheses that Archaea-Specific primers would offer higher resolution of archaeal diversity and that the four ecologically distinct host species would have distinct archaeal communities. Archaea-Specific primers resulted in increases in archaeal richness and detection of Archaea in all four birds compared to the Universal primers. The ammonia-oxidizing archaeal order Nitrososphaerales was detected in all four host species, and methanogenic orders were enriched in samples from Canada Geese. In Bacteria-Archaea co-occurrence networks, Archaea-Specific primers found many more significant interactions than the Universal primers alone. Methanogenic archaeal orders dominated the microbiota in Canada Geese and were found to a lesser extent in the other host species, suggesting an important functional role of methanogens in Canada Geese. Overall, this study advances our knowledge of the archaeal component of the microbiome in wild birds and provides insight into the potential functional roles Archaea play in studies of avian gastrointestinal microbiota.

IMPORTANCE

Archaea may be persistent members of host-associated microbiomes across diverse host taxa; their detection has been limited due to their low abundance and the inadequacy of Universal primers. Large-scale studies of Archaea in vertebrate microbiomes have historically had low intraspecific sample sizes for bird species and had conflicting results. This study demonstrates the improved capability of the Archaea-Specific primers to detect archaeal diversity in diverse avian host species compared to the widely used Universal primers. We also identified both shared and species-specific archaeal taxa across four ecologically distinct avian host species from four different orders with implications for functional importance. Future studies interested in comprehensively cataloging prokaryotic diversity in avian microbiomes using amplicon-based sequencing methods should include Archaea-Specific primers to adequately probe archaeal diversity.

Targeted Nutritional Metabolomic Analysis of Marine Species (Tursiops truncatus, Phoca vitulina, Otaria flavescens and Pygoscelis papua)

Ecological nutrition aims to unravel the extensive web of nutritional links that drive animals in their interactions with their habitat. Metabolomic profiling of species could increase the knowledge of their ecology, as well as allowing us to better understand the interactions of environment, including distribution, availability of food and fitness of the species, among others. Metabolomic profile is affected by several causes such as nutrition, physiological status, metabolism and species. Thus, the main aim of this work will be to provide, for the first time, values of the nutritional metabolome profile in marine species, as well as to study the differences in the metabolomic profile due to the classification group. To achieve this, blood samples from marine animals (n = 55) were used in this experiment, including Gentoo penguin (Pygoscelis papua), Patagonian sea lion (Otaria flavescens), Harbour seal (Phoca vitulina) and Bottlenose dolphin (Tursiops truncatus). Blood samples were analysed to determine the nutritional metabolites, specifically non-esterified fatty acid (NEFA), glucose, triglyceride, uric acid, cholesterol, albumin, total protein and inorganic phosphorous (iP). Pygoscelis papua exhibited the most statistically significant differences compared to the other groups, showing higher levels of plasma glucose, triglycerides, uric acid, and cholesterol, and lower levels of albumin, total protein, urea, and iP relative to the average values (simple means) observed in the other species. Also, it can be concluded that nutritional metabolome of Tursiops truncatus is different from that of Otaria flavescens, due to the differences in urea and albumin. These results show the potential of metabolomics to elucidate the relationship between metabolism and external factors in species. However, more molecular ecology studies are necessary to deepen the study of the interrelationships between the environment and metabolism, with the aim of including this tool in specific programmes for conservation and biological study.

Isolation and identification of uric acid-dependent Aciduricibacillus chroicocephali gen. nov., sp. nov. from seagull feces and implications for hyperuricemia treatment

Hyperuricemia has become the second most prevalent metabolic disease after diabetes, but the limitations of urate-lowering treatment (ULT) drugs and patient nonadherence make ULT far less successful. Thus, more ULT approaches urgently need to be explored. Uric acid-degrading bacteria have potential application value in ULT. In this study, we isolated 44XBT, a uric acid-degrading bacterium, from black-headed gull (Chroicocephalus ridibundus) feces. Using a polyphasic taxonomic approach, strain 44XBT was identified as a novel genus within the family Bacillaceae; subsequently, the name Aciduricibacillus chroicocephali was proposed. Strain 44XBT had a unique uric acid-dependent phenotype and utilized uric acid and allantoin as the sole carbon and nitrogen sources, but not common carbon sources or complex media. In the genome, multiple copies of genes involved in uric acid metabolic pathway (pucL, pucM, uraD, and allB) were found. Six copies of pucL (encoding urate oxidase) were detected. Of these, five pucL copies were in a tandem arrangement and shared 70.42%-99.70% amino acid identity. In vivo experiments revealed that 44XBT reduced serum uric acid levels and attenuated kidney damage in hyperuricemic mice through uric acid catalysis in the gut and gut microbiota remodeling. In conclusion, our findings discover a strain for studying bacterial uric acid metabolism and may provide valuable insights into ULT.

IMPORTANCE

The increasing disease burden of hyperuricemia highlights the need for new therapeutic drugs and treatment strategies. Our study describes the developmental and application values of natural uric acid-degrading bacteria found in the gut of birds and broadened the source of bacteria with potential therapeutic value. Furthermore, the special physiology characteristics and genomic features of strain 44XBT are valuable for further study.

Cysteine Enrichment Mediates Co-Option of Uricase in Reptilian Skin and Transition to Uricotelism

Uric acid is the main means of nitrogen excretion in uricotelic vertebrates (birds and reptiles) and the end product of purine catabolism in humans and a few other mammals. While uricase is inactivated in mammals unable to degrade urate, the presence of orthologous genes without inactivating mutations in avian and reptilian genomes is unexplained. Here we show that the Gallus gallus gene we name cysteine-rich urate oxidase (CRUOX) encodes a functional protein representing a unique case of cysteine enrichment in the evolution of vertebrate orthologous genes. CRUOX retains the ability to catalyze urate oxidation to hydrogen peroxide and 5-hydroxyisourate (HIU), albeit with a 100-fold reduced efficiency. However, differently from all uricases hitherto characterized, it can also facilitate urate regeneration from HIU, a catalytic property that we propose depends on its enrichment in cysteine residues. X-ray structural analysis highlights differences in the active site compared to known orthologs and suggests a mechanism for cysteine-mediated self-aggregation under H2O2-oxidative conditions. Cysteine enrichment was concurrent with the transition to uricotelism and a shift in gene expression from the liver to the skin where CRUOX is co-expressed with β-keratins. Therefore, the loss of urate degradation in amniotes has followed opposite evolutionary trajectories: while uricase has been eliminated by pseudogenization in some mammals, it has been repurposed as a redox-sensitive enzyme in the reptilian skin.

Microbial gene expression during hibernation in arctic ground squirrels: greater differences across gut sections than in response to pre-hibernation dietary protein content

Obligate seasonal hibernators fast for 5-9 months depending on species yet resist muscle atrophy and emerge with little lean mass loss. The role of the gut microbiome in host nitrogen metabolism during hibernation is therefore of considerable interest, and recent studies support a role for urea nitrogen salvage (UNS) in host-protein conservation. We were interested in the effect of pre-hibernation diet on UNS and the microbial provision of essential amino acids (EAAs) during hibernation; therefore, we conducted a study whereby we fed arctic ground squirrels (Urocitellus parryii) pre-hibernation diets containing 9% vs. 18% protein and compared the expression of gut bacterial urease and amino acid (AA) metabolism genes in 4 gut sections (cecum mucosa, cecum lumen, small intestine [SI] mucosa, and SI lumen) during hibernation. We found that pre-hibernation dietary protein content did not affect expression of complete bacterial AA pathway genes during hibernation; however, several individual genes within EAA pathways were differentially expressed in squirrels fed 18% pre-hibernation dietary protein. Expression of genes associated with AA pathways was highest in the SI and lowest in the cecum mucosa. Additionally, the SI was the dominant expression site of AA and urease genes and was distinct from other sections in its overall microbial functional and taxonomic composition. Urease expression in the gut microbiome of hibernating squirrels significantly differed by gut section, but not by pre-hibernation dietary protein content. We identified two individual genes that are part of the urea cycle and involved in arginine biosynthesis, which were significantly more highly expressed in the cecum lumen and SI mucosa of squirrels fed a pre-hibernation diet containing 18% protein. Six bacterial genera were responsible for 99% of urease gene expression: Cupriavidus, Burkholderia, Laribacter, Bradhyrizobium, Helicobacter, and Yersinia. Although we did not find a strong effect of pre-hibernation dietary protein content on urease or AA metabolism gene expression during hibernation, our data do suggest the potential for pre-hibernation diet to modulate gut microbiota function during hibernation, and further investigations are warranted.

Lactobacillus (L. plantarum & L. rhamnosus) and Saccharomyces (S. cerevisiae): effects on performance, biochemical parameters, ammonium ion in manure, and digestibility of broiler chickens

Two strains of Lactobacillus combined with Baker's yeast (Saccharomyces cerevisiae) used as probiotics were evaluated to replace antibiotics in poultry flocks by reducing ammonia emissions in manure of broilers without comprising performance or health. One-day-old Cobb 500 broilers (600) were fed starter, grower, and finisher diets as control (CON); probiotic S. cerevisiae, inclusion rate at 4.26 × 10⁶ CFU/kg of feed (SCY); probiotic L. plantarum and L. rhamnosus, inclusion rate at 4.35 × 10⁸ CFU/kg of feed (LPR) for each; and a combination of Lactobacillus plantarum and L. rhamnosus at 4.35 × 10⁸ CFU/kg of feed for each plus Saccharomyces cerevisiae and 4.26 × 10⁶ CFU/kg of feed (SWL). The 4 treatments had 5 replicates (pens), each with 30 broilers. Performance was measured weekly as feed consumption, weight gain, BW, and feed conversion ratio (FCR) over a 6-wk grow-out period. Accompanying biochemical analyses included lipase activity of the pancreas, liver weight, and uric acid (UA) concentration in liver. Albumin, total protein, UA, ammonia, and blood urea nitrogen (BUN) were measured in serum. Ammonium (NH₄⁺) in manure and apparent ileal digestibility from digesta were also measured. Significance was determined at P ≤ 0.05. Results showed that biochemical analyses had no significant treatment effect; however, there were significant temporal changes in performance measures for individual treatments. Feed consumption increased over time for all treatments (P = 2.00 × 10^-16). CON had lower weight gain in wk 2 (P = 0.013) compared to all treatment and the lowest BW in wk 5 (P = 0.0008) and wk 6 (P = 0.0124) compared to SWL. Specific probiotic strains, with well-defined inclusion rates, and surrounding environmental analyses of present microbes are needed to ascertain effects of probiotics. Other important areas for investigation include 1) confirmation of probiotics present in the digesta/ceca and how they alter the microbiota within the gastrointestinal (GI) tract and 2) the serum heterophil:lymphocyte ratio to further examine potential immune responses to the probiotics.

Effects of Post-Ruminal Urea Supplementation during the Seasonal Period on Performance and Rumen Microbiome of Rearing Grazing Nellore Cattle

The objective was to evaluate the effects of urea with post-ruminal absorption in the supplementation of growing Nellore cattle reared on pasture during a seasonal period. For the study, two experiments were conducted. In experiment 1, rumen and blood parameters were evaluated using eight rumen-cannulated Nellore bulls with initial body weight (BW) of 763 ± 44 kg, distributed in a double Latin square 4 × 4. In experiment 2, 120 Nellore steers with initial BW of 380 ± 35 kg were used for performance evaluation, distributed in a randomized block design (blocking factor or initial BW). The evaluated treatments were 1: (TP-U) (control) = supplement with 24% crude protein (CP) containing urea as a source of non-protein nitrogen (NPN; 3%) and soybean meal, 2: (TP-PRU) = 24% CP supplement containing post-ruminal urea (PRU; 3.6%) and soybean meal; 3: (NPN-U-PRU) = 24% CP supplement containing urea + post-ruminal urea (U = 3% and PRU = 3.9%), without soybean meal; 4: (NPN-PRU) = supplement with 24% CP containing post-ruminal urea (7.5%), without soybean meal. The supplement was offered at 3 g/kg BW per animal, daily, once a day. All animals were kept on Urochloa brizantha cv. Marandu pasture. Statistical analyses were performed using the SAS PROC MIXED, and the data were evaluated by the following contrasts: C1 = TP-U/TP-PRU vs. NPN-U-PRU/NPN-PRU (Soybean meal replacement by NPN); C2 = TP-U vs. TP-PRU (conventional urea vs. post-immune urea); C3 = NPN-U-PRU vs. NPN-PRU (low and high post-ruminal urea-PRU level). The digestibility of dry matter, organic matter, and NDF was lower when soybean meal was replaced by non-protein nitrogen, also being different between the levels of post-ruminal urea used in the supplement. Ruminal pH was different when soybean meal was replaced by NPN (p = 0.003). Total concentration of short-chain fatty acids, concentrations of isobutyrate (p = 0.003), valerate (p = 0.001), and isovalerate (p = 0.001) were different, and blood urea was different when soybean meal was replaced by NPN (p = 0.006). Simpson's diversity index was higher in the rumen of animals supplemented with TP-U than in those supplemented with TP-PRU (p = 0.05). A total of 27 phyla, 234 families, and 488 genera were identified. Nitrospirota and Gemmatimonadota phyla were detected just in the rumen of steers supplemented with TP-PRU. The performance (final BW, weight gain and gain per area) of the animals was different, being higher (p = 0.04) in animals supplemented with soybean meal, compared to NPN. The removal of soybean meal from the supplement and its replacement with either conventional urea plus post-ruminal urea or only post-ruminal urea compromises the performance of the animals. The lower the post-ruminal urea inclusion level, the lower the apparent digestibility of dry matter, organic matter, and NDF, when compared to animals supplemented with higher levels.

Sodium butyrate reduces ammonia production in the cecum of laying hens by regulating ammonia-producing bacteria

Sodium butyrate is a commonly used feed additive and can reduce ammonia (NH₃) emissions from laying hens, but the mechanism of this effect is unknown. In this study, the sodium butyrate and cecal content of Lohmann pink laying hens were measured, and in vitro fermentation experiments and NH₃-producing bacteria coculture experiments were carried out to explore the relationship between NH₃ emissions and its associated microbiota metabolism. Sodium butyrate was found to significantly reduce NH₃ emission from the cecal microbial fermentation of Lohmann pink laying hens (P < 0.05). The concentration of NO₃^--N in the fermentation broth of the sodium butyrate-supplemented group increased significantly, and the concentration of NH₄⁺-N decreased significantly (P < 0.05). Moreover, sodium butyrate significantly reduced the abundance of harmful bacteria and increased the abundance of beneficial bacteria in the cecum. The culturable NH₃-producing bacteria consisted mainly of Escherichia and Shigella, such as Escherichia fergusonii, Escherichia marmotae and Shigella flexnerii. Among them, E. fergusonii had the highest potential for NH₃ production. The coculture experiment showed that sodium butyrate can significantly downregulate the expression of the lpdA, sdaA, gcvP, gcvH and gcvT genes of E. fergusonii (P < 0.05), thus reducing the NH₃ emission produced by the bacteria during metabolism. In general, sodium butyrate regulated NH₃-producing bacteria to reduce NH₃ production in the cecum of laying hens. These results are of great significance for NH₃ emission reduction in the layer breeding industry and for future research.

Delayed access to feed early post-hatch affects the development and maturation of gastrointestinal tract microbiota in broiler chickens

Background

The first two weeks of post-hatch (PH) growth in broilers (meat-type birds) are critical for gut development and microbiota colonization. In the current broiler production system, chicks may not receive feed and water for 24 to 72 h due to variations in hatching time and hatchery management. Post-hatch feed delay affects body weight, feed efficiency, mortality, and gut development. The goal of this study was to investigate changes in the microbiome in broiler chickens early PH and the effect of delayed access to feed on the microbiota.

Results

Chicks either received feed and water immediately after hatch or access to feed was delayed for 48 h to mimic commercial hatchery settings (treatment, TRT). Both groups were sampled (n = 6) at -48, 0, 4 h, and 1 (24 h), 2 (48 h), 3 (72 h), 4 (96 h), 6 (144 h), 8 (192 h), 10 (240 h), 12 (288 h) and 14 (336 h) days PH. Ileal (IL) and cecal (CE) epithelial scrapings (mucosal bacteria, M) and digesta (luminal bacteria, L) were collected for microbiota analysis. Microbiota was determined by sequencing the V3-V4 region of bacterial 16S rRNA and analyzed using QIIME2. The microbiota of early ileal and cecal samples were characterized by high abundance of unclassified bacteria. Among four bacterial populations (IL-L, IL-M, CE-L, CE-M), IL-M was the least affected by delayed access to feed early PH. Both alpha and beta diversities were affected by delayed access to feed PH in IL-L, CE-M and CE-L. However, the development effect was more pronounced. In all four bacterial populations, significant changes due to developmental effect (time relative to hatch) was observed in taxonomic composition, with transient changes of bacterial taxa during the first two weeks PH. Delayed access to feed has limited influence on bacterial composition with only a few genera and species affected in all four bacterial populations. Predicted function based on 16S rRNA was also affected by delayed access to feed PH with most changes in metabolic pathway richness observed in IL-L, CE-L and CE-M.

Conclusions

These results show transient changes in chicken microbiota biodiversity during the first two weeks PH and indicate that delayed access to feed affects microbiota development. Proper microbiota development could be an important factor in disease prevention and antibiotic use in broiler chickens. Moreover, significant differences in response to delayed access to feed PH between luminal and mucosal bacterial populations strongly suggests the need for separate analysis of these two populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02619-6.

The gut microbiome may influence post-prandial nitrogen handling in an elasmobranch, the Pacific spiny dogfish (Squalus suckleyi)

Nitrogen recycling through the gut microbiome is an important mechanism used throughout vertebrates to reclaim valuable nitrogen trapped in urea. Evidence suggests it may be especially important in nitrogen limited animals, yet little is known about its role in marine elasmobranchs, which are said to be severely nitrogen limited. In the present study we used antibiotics to deplete the gut microbiome of Pacific spiny dogfish and assessed the role of the microbiome in nitrogen handling in both fed and fasted states. In fed animals, antibiotic treatment eliminated the activity of the microbial enzyme urease and reduced cellulase activity by 78%. This reduction in microbial enzyme activity resulted in significantly lower plasma urea levels which then trended upward as urea excretion rates decreased. Ammonia excretion rates were also significantly lower in antibiotic treated fish compared to the control fed. Finally, antibiotic treated fed individuals lost an average of 7.4% of their body mass while the fed controls lost only 1.8% of their body mass. Nitrogen handling in fasted animals was not significantly impacted by a reduction in microbial activity. These results suggest that compromising the gut microbiome significantly influences post-prandial nitrogen handling in spiny dogfish, and that the recycling of urea‑nitrogen may be vital to maintaining nitrogen balance in these fish.

Reflux of 15N-labeled uric acid after intracloacal infusion in broiler chickens fed low- or high-protein diets

Reflux of urine from the cloaca into the ceca provides chickens with a mechanism for recycling of urinary-Nitrogen (N) in a way analogous to urea recycling in mammals. However, it is unknown if reflux has substantial relevance in current poultry husbandry, where birds are fed ad libitum and have high protein intake. To evaluate the fate of urinary-N in ad libitum-fed broiler chickens, 15-day-old broilers were assigned to a high (21.9% CP, n = 22) or low (10.2 % CP, n = 22) protein diet. At 25 d of age, 20 broilers per dietary treatment were infused into the cloaca with a pulse dose of 107 mg [1,3-¹⁵N]-uric acid. N-contents and ¹⁵N-enrichment in digesta, blood plasma, and body tissues were measured at 5, 30, 60, 90, 150, 300, 450, 600, 1,200, or 1,800 min after administration (n = 2 /time-point /diet). Two broilers per dietary treatment were infused with saline and served as control to analyze background ¹⁵N-enrichment. The average total recovery (% of infused (w/w)) of ¹⁵N from infused uric acid in all body tissues was low (2.9 ± 0.62 %), of which the largest proportion was found in carcass tissue (2.5 ± 0.60%). ¹⁵N-enrichment was greatest in intestinal tissues. Even at 1,200 min, ¹⁵N-enrichment of ceca (0.46 ± 0.169 APE) and colon (0.13 ± 0.159 APE) digesta was considerably exceeding background enrichment. ¹⁵N-enrichment in excess of background enrichment in cecum and colon digesta (10-fold, P < 0.05), and ¹⁵N recovery in intestinal tissues (4-fold, P < 0.01) were greater in birds fed the low protein diet compared with the high protein diet, speculatively pointing out differences in the occurrence of reflux, incorporation of uric acid-N derivatives in intestinal tissues by first-pass metabolism, and a prolonged digesta retention time in protein deficient birds. In conclusion, these data confirm that uric acid-N infused in the cloaca can be refluxed and used for body N-deposition, but its contribution to whole body protein metabolism in broilers is probably limited.

Development and validation of a highly effective analytical method for the evaluation of the exposure of migratory birds to antibiotics and their metabolites by faeces analysis

The widespread occurrence of antibiotics in the environment may exert a negative impact on wild organisms. In addition, they can become environmental reservoirs, through the ingestion of food or contaminated water, and vectors for antibiotic-resistant bacteria. This fact is even more important in migratory birds that can promote their dissemination across continents. In this work, a multiresidue analytical method suitable for the determination of five families of antibiotics and their main metabolites in waterbird faeces has been developed and validated. The target compounds include environmentally significant sulfonamides, macrolides, fluoroquinolones, tetracyclines and antifolates. Sample treatment involves ultrasound-assisted extraction with methanol and dispersive solid-phase extraction clean-up with C18. Analytical determination was carried out by liquid chromatography-tandem mass spectrometry. The most significant parameters affecting sample extraction and extract clean-up were optimised by means of experimental designs. Good linearity (R² > 0.994), accuracy (from 41 to 127%), precision (relative standard deviation lower than 24%) and limits of quantification (lower than 2 ng g^-1 (dry weight, dw)) were obtained for most of the compounds. The method was applied to the determination of the selected compounds in 27 faeces samples from three common migratory waterbird species. Nine antibiotics and three of their metabolites were detected in the analysed samples. Fluoroquinolones and macrolides were the antibiotics most frequently detected. The highest concentrations corresponded to norfloxacin (up to 199 ng g^-1 dw).

Chelonian Sedation and Anesthesia

Anesthetic management of chelonians represents a unique challenge; the order Chelonia includes numerous species that display diverse anatomic features, habitats, body sizes, temperaments, and metabolic rates. Owing to their peculiar characteristics, safe and effective sedation and anesthesia may be more complicated than in other animals. For example, gas inductions are not indicated, and intravenous catheterization requires practice. The pharmacology of anesthetic drugs is severely impacted by body/environmental temperature, site of administration, and organ function. This review will summarize the current knowledge in terms of anatomy, physiology, and drug metabolism in chelonians, before discussing practical aspects of anesthesia.

A Critical Review of Morphologic Findings and Data From 14 Toxicological Studies Involving Fish Exposures to Diclofenac

A number of studies have investigated the potential toxicity of the analgesic agent diclofenac (DCF) in various fish species under a diverse array of experimental conditions. Reported evidence of toxicity in these investigations is often strongly reliant on morphologic end points such as histopathology, immunohistochemistry, and transmission electron microscopy. However, it may be challenging for scientists who perform environmental hazard or risk determination to fully appreciate the intricacies of these specialized endpoints. Therefore, the purpose of the current review was to critically assess the quality of morphologic data in 14 papers that described the experimental exposure of fish to DCF. Areas of focus during this review included study design, diagnostic accuracy, magnitude of reported changes, data interpretation and presentation, and the credibility of individual reported findings. Positive attributes of some studies included robust experimental designs, accurate diagnoses, and straightforward and transparent data reporting. Issues identified in certain articles included diagnostic errors, failure to account for sampling and/or observer bias, failure to evaluate findings according to sex, exaggeration of lesion severity, interstudy inconsistencies, unexplained phenomena, and incomplete or ambiguous data presentation. It is hoped that the outcome of this review will be of value for personnel involved in regulatory decision-making.

A review of reductionist methods in fish gastrointestinal tract physiology

A holistic understanding of a physiological system can be accomplished through the use of multiple methods. Our current understanding of the fish gastrointestinal tract (GIT) and its role in both nutrient handling and osmoregulation is the result of the examination of the GIT using multiple reductionist methods. This review summarizes the following methods: in vivo mass balance studies, and in vitro gut sac preparations, intestinal perfusions, and Ussing chambers. From Homer Smith's initial findings of marine fish intestinal osmoregulation in the 1930s through to today's research, we discuss the methods, their advantages and pitfalls, and ultimately how they have each contributed to our understanding of fish GIT physiology. Although in vivo studies provide substantial information on the intact animal, segment specific functions of the GIT cannot be easily elucidated. Instead, in vitro gut sac preparations, intestinal perfusions, or Ussing chamber experiments can provide considerable information on the function of a specific tissue and permit the delineation of specific transport pathways through the use of pharmacological agents; however, integrative inputs (e.g. hormonal and neuronal) are removed and only a fraction of the organ system can be studied. We conclude with two case studies, i) divalent cation transport in teleosts and ii) nitrogen handling in the elasmobranch GIT, to highlight how the use of multiple reductionist methods contributes to a greater understanding of the organ system as a whole.

Urea supplementation in rumen and post-rumen for cattle fed a low-quality tropical forage

We evaluated the differences between the supplementation of urea in rumen and/or abomasum on forage digestion, N metabolism and urea kinetics in cattle fed a low-quality tropical forage. Five Nellore heifers were fitted with rumen and abomasum fistulas and assigned to a Latin square design. The treatments were control, continuous infusion of urea in the abomasum (AC), continuous infusion of urea in the rumen, a pulse dose of urea in the rumen every 12 h (PR) and a combination of PR and AC. The control exhibited the lowest (P < 0·10) faecal and urinary N losses, which were, overall, increased by supplementation. The highest urinary N losses (P < 0·10) were observed when urea was either totally or partially supplied as a ruminal pulse dose. The rumen N balance was negative for the control and when urea was totally supplied in the abomasum. The greatest microbial N production (P < 0·10) was obtained when urea was partially or totally supplied in the abomasum. Urea supplementation increased (P < 0·10) the amount of urea recycled to the gastrointestinal tract and the amount of urea-N returned to the ornithine cycle. The greatest (P < 0·10) amounts of urea-N used for anabolism were observed when urea was totally and continuously infused in the abomasum. The continuous abomasal infusion also resulted in the highest (P < 0·10) assimilation of microbial N from recycling. The continuous releasing of urea throughout day either in the rumen or abomasum is able to improve N accretion in the animal body, despite mechanism responsible for that being different.

Optimal integration between host physiology and functions of the gut microbiome

Host-associated microbial communities have profound impacts on animal physiological function, especially nutrition and metabolism. The hypothesis of 'symmorphosis', which posits that the physiological systems of animals are regulated precisely to meet, but not exceed, their imposed functional demands, has been used to understand the integration of physiological systems across levels of biological organization. Although this idea has been criticized, it is recognized as having important heuristic value, even as a null hypothesis, and may, therefore, be a useful tool in understanding how hosts evolve in response to the function of their microbiota. Here, through a hologenomic lens, we discuss how the idea of symmorphosis may be applied to host-microbe interactions. Specifically, we consider scenarios in which host physiology may have evolved to collaborate with the microbiota to perform important functions, and, on the other hand, situations in which services have been completely outsourced to the microbiota, resulting in relaxed selection on host pathways. Following this theoretical discussion, we finally suggest strategies by which these currently speculative ideas may be explicitly tested to further our understanding of host evolution in response to their associated microbial communities. This article is part of the theme issue 'The role of the microbiome in host evolution'.

Hypothalamic-Pituitary-Thyroid Axis Crosstalk With the Hypothalamic-Pituitary-Gonadal Axis and Metabolic Regulation in the Eurasian Tree Sparrow During Mating and Non-mating Periods

Reproduction is an energetically costly phenomenon. Therefore, to optimize reproductive success, male birds invest enough energetic resources for maintaining well-developed testes. The hypothalamic-pituitary-thyroid (HPT) axis in birds can crosstalk with the hypothalamic-pituitary-gonadal (HPG) axis, thus orchestrating both the reproduction and metabolism. However, until now, how the free-living birds timely optimize both the energy metabolism and reproduction via HPT-axis is not understood. To uncover this physiological mechanism, we investigated the relationships among body mass, testis size, plasma hormones including thyroid-stimulating hormone (TSH), thyroxine (T₄), triiodothyronine (T₃), metabolites including glucose (Glu), triglyceride (TG), total cholesterol (TC), uric acid (UA), diencephalon mRNA expressions of type 2 (Dio2) and 3 (Dio3) iodothyronine deiodinase enzymes, thyrotropin-releasing hormone (TRH), thyroid-stimulating hormone (TSH), gonadotropin-releasing hormone I (GnRH-I), and gonadotropin-inhibitory hormone (GnIH) in a male Eurasian tree sparrow (ETS, Passer montanus). We found significantly larger testis size; elevated diencephalon Dio2 and TRH mRNA expressions, plasma T₃, and UA levels; and significantly lowered Glu, TG, and TC levels during mating relative to the non-mating stages in male ETSs. However, Dio3, TSH, GnRH-I, and GnIH mRNA expression did not vary with the stage. Furthermore, life-history stage dependent variation in plasma T₃ had both direct effects on the available energy substrates and indirect effects on body mass and testis size, indicating a complex regulation of metabolic pathways through the HPT- and HPG-axes. The identified differences and relationships in mRNA expression, plasma T₃ and metabolites, and testis size in male ETSs contribute to our understanding how free-living birds adjust their molecular, endocrinal, and biochemical features to orchestrate their reproductive physiology and metabolism for the maintenance of well-developed testes.

Short-term exposure to 12‰ brackish water has significant effects on the endocrine physiology of juvenile American alligator (Alligator mississippiensis)

American alligators (Alligator mississippiensis) mainly inhabit freshwater habitats but can be exposed to a wide range of salinities during storm surges, droughts or from alterations in freshwater flows. Although some salinization events last weeks, others only last a few days. This study assessed changes in the endocrine function of the renin-angiotensin-aldosterone system (RAAS) and steroid hormone production (steroidogenesis) in juvenile alligators exposed to brackish water (12‰) for 7 days. We quantified plasma levels of angiotensin II and the corticosteroids (aldosterone, corticosterone and 11-deoxycortisol). Various progestogens, androgens, and estrogens were further assessed. The protein expression for the RAAS enzymes, renin and angiotensin converting enzyme (ACE), was quantified immunohistochemically in kidney and lung tissue, respectively, and histology was performed on kidney, lung and gonad tissues. Finally, blood biochemistry parameters such as electrolyte levels and diagnostic indicators for dehydration, renal, and hepatic function were measured. Corticosterone, 11-deoxycortisol, Na⁺, Cl^-, total protein, albumin, uric acid, and cholesterol levels were all significantly elevated in alligators exposed to brackish water compared with alligators in freshwater. The levels of 17β-estradiol and estrone were significantly lowered while histology showed alterations in gonad tissue in the brackish water exposed group. In contrast, while there were no effects of exposure on aldosterone levels, angiotensin II was significantly reduced in brackish water exposed alligators. These results correlated with significantly decreased expressions for both renin and ACE in kidney and lung tissue. Overall, this study showed that short-term exposure of alligators to 12‰ brackish water has significant endocrine effects on juvenile alligators.

Urea hydrolysis by gut bacteria in a hibernating frog: evidence for urea-nitrogen recycling in Amphibia

Gut bacteria that produce urease, the enzyme hydrolysing urea, contribute to nitrogen balance in diverse vertebrates, although the presence of this system of urea-nitrogen recycling in Amphibia is as yet unknown. Our studies of the wood frog (Rana sylvatica), a terrestrial species that accrues urea in winter, documented robust urease activity by enteric symbionts and hence potential to recoup nitrogen from the urea it produces. Ureolytic capacity in hibernating (non-feeding) frogs, whose guts hosted an approximately 33% smaller bacterial population, exceeded that of active (feeding) frogs, possibly due to an inductive effect of high urea on urease expression and/or remodelling of the microbial community. Furthermore, experimentally augmenting the host's plasma urea increased bacterial urease activity. Bacterial inventories constructed using 16S rRNA sequencing revealed that the assemblages hosted by hibernating and active frogs were equally diverse but markedly differed in community membership and structure. Hibernating frogs hosted a greater relative abundance and richer diversity of genera that possess urease-encoding genes and/or have member taxa that reportedly hydrolyse urea. Bacterial hydrolysis of host-synthesized urea probably permits conservation and repurposing of valuable nitrogen not only in hibernating R. sylvatica but, given urea's universal role in amphibian osmoregulation, also in virtually all Amphibia.

Nitrogen handling in the elasmobranch gut: a role for microbial urease

Ureotelic elasmobranchs require nitrogen for both protein growth and urea-based osmoregulation, and therefore are probably nitrogen-limited in nature. Mechanisms exist for retaining and/or scavenging nitrogen in the gills, kidney, rectal gland and gut, but as yet, the latter are not well characterized. Intestinal sac preparations of the Pacific spiny dogfish shark (Squalus acanthias suckleyi) incubated in vitro strongly reabsorbed urea from the lumen after feeding, but mucosal fluid ammonia concentrations increased with incubation time. Phloretin (0.25 mmol l^-1, which blocked urea reabsorption) greatly increased the rate of ammonia accumulation in the lumen. A sensitive [¹⁴C]urea-based assay was developed to examine the potential role of microbial urease in this ammonia production. Urease activity was detected in chyme/intestinal fluid and intestinal epithelial tissue of both fed and fasted sharks. Urease was not present in gall-bladder bile. Urease activities were highly variable among animals, but generally greater in chyme than in epithelia, and greater in fed than in fasted sharks. Comparable urease activities were found in chyme and epithelia of the Pacific spotted ratfish (Hydrolagus colliei), a ureotelic holocephalan, but were much lower in ammonotelic teleosts. Urease activity in dogfish chyme was inhibited by acetohydroxamic acid (1 mmol l^-1) and by boiling. Treatment of dogfish gut sac preparations with acetohydroxamic acid blocked ammonia production, changing net ammonia accumulation into net ammonia absorption. We propose that microbial urease plays an important role in nitrogen handling in the elasmobranch intestine, allowing some urea-N to be converted to ammonia, which is then reabsorbed for amino acid synthesis or reconversion to urea.

Non-invasive monitoring of glucocorticoid metabolite concentrations in urine and faeces of the Sungazer (Smaug giganteus)

Developing non-invasive techniques for monitoring physiological stress responses has been conducted in a number of mammal and bird species, revolutionizing field-based endocrinology and conservation practices. However, studies validating and monitoring glucocorticoid concentrations in reptiles are still limited. The aim of the study was to validate a method for monitoring glucocorticoid metabolite concentrations in urine (uGCM) and faeces (fGCM) of the cordylid lizard, the Sungazer (Smaug giganteus). An adrenocorticotropic hormone (ACTH) challenge was conducted on one male and two females with both urine and faecal material being collected during baseline and post-injection periods. Steroid extracts were analysed with four enzyme immunoassays (EIAs)namely: 11-oxoaetiocholanolone, 5α-pregnane-3β-11β-21-triol-20-one, tetrahydrocorticosterone, and corticosterone. A considerable response in fGCM and uGCM concentrations following ACTH administration was observed in all subjects, with the 5α-pregnane-3β-11β-21-triol-20-one and tetrahydrocorticosterone EIAs appearing to be the most suited for monitoring alterations in glucocorticoid metabolite concentrations in S. giganteus using faeces or urine as hormone matrix. Both EIAs showed a significantly higher concentration of glucocorticoid metabolites in faeces compared to urine for both sexes. Collectively, the findings of this study confirmed that both urine and faeces can be used to non-invasively assess adrenocortical function in S. giganteus.

Overwintering adaptations and extreme freeze tolerance in a subarctic population of the wood frog, Rana sylvatica

The terrestrially hibernating wood frog (Rana sylvatica) is well-known for its iconic freeze tolerance, an overwintering adaptation that has received considerable investigation over the past 35 years. Virtually, all of this research has concerned frogs indigenous to the temperate regions of its broad range within North America. However, recent investigations have shown that frogs of subarctic populations are extremely cold hardy, being capable of surviving freezing for longer periods and at much lower temperatures as compared to conspecifics from temperate regions. Their exceptional freeze tolerance is partly supported by an enhanced cryoprotectant system that uses very high levels of urea and glucose to limit ice formation, regulate metabolism, and protect macromolecules and cellular structures from freezing/thawing stresses. In the weeks before they begin hibernating, northern frogs undertake radical physiological transitions, such as depletion of fat stores and catabolism of muscle protein, that prime the cryoprotectant system by accruing urea and stockpiling glycogen from which glucose is mobilized during freezing. Concentrations of cryoprotectants ultimately achieved in Alaskan frogs when freezing occurs vary among tissues but generally are higher than those of frogs inhabiting milder climates. This review summarizes the molecular, biochemical, and physiological adaptations permitting this northern phenotype to survive the long and harsh winters of the region.

Comparison of gizzard and intestinal microbiota of wild neotropical birds

Gut bacterial communities have been shown to be influenced by diet, host phylogeny and anatomy, but most of these studies have been done in captive animals. Here we compare the bacterial communities in the digestive tract of wild birds. We characterized the gizzard and intestinal microbiota among 8 wild Neotropical bird species, granivorous or frugivorous species of the orders Columbiformes and Passeriformes. We sequenced the V4 region of the 16S rRNA gene in 94 collected samples from 32 wild birds from 5 localities, and compared bacterial communities by foraging guild, organ, locality and bird taxonomy. 16S rRNA gene-based sequencing data were examined using QIIME with linear discriminant analysis effect size (LEfSe) and metabolic pathways were predicted using PICRUSt algorism. We identified 8 bacterial phyla, dominated by Firmicutes, Actinobacteria and Proteobacteria. Beta diversity analyses indicated significant separation of gut communities by bird orders (Columbiformes vs. Passerifomes) and between bird species (p<0.01). In lower intestine, PICRUSt shows a predominance of carbohydrate metabolism in granivorous birds and xenobiotics biodegradation pathways in frugivorous birds. Gizzard microbiota was significantly richer in granivorous, in relation to frugivorous birds (Chao 1; non-parametric t-test, p<0.05), suggesting a microbial gizzard function, beyond grinding food. The results suggest that the most important factor separating the bacterial community structure was bird taxonomy, followed by foraging guild. However, variation between localities is also likely to be important, but this could not been assessed with our study design.

A place for host-microbe symbiosis in the comparative physiologist's toolbox

Although scientists have long appreciated that metazoans evolved in a microbial world, we are just beginning to appreciate the profound impact that host-associated microbes have on diverse aspects of animal biology. The enormous growth in our understanding of host-microbe symbioses is rapidly expanding the study of animal physiology, both technically and conceptually. Microbes associate functionally with various body surfaces of their hosts, although most reside in the gastrointestinal tract. Gut microbes convert dietary and host-derived substrates to metabolites such as short-chain fatty acids, thereby providing energy and nutrients to the host. Bacterial metabolites incorporated into the host metabolome can activate receptors on a variety of cell types and, in doing so, alter host physiology (including metabolism, organ function, biological rhythms, neural activity and behavior). Given that host-microbe interactions affect diverse aspects of host physiology, it is likely that they influence animal ecology and, if they confer fitness benefits, the evolutionary trajectory of a species. Multiple variables - including sampling regime, environmental parameters, host metadata and analytical methods - can influence experimental outcomes in host-microbiome studies, making careful experimental design and execution crucial to ensure reproducible and informative studies in the laboratory and field. Integration of microbiomes into comparative physiology and ecophysiological investigations can reveal the potential impacts of the microbiota on physiological responses to changing environments, and is likely to bring valuable insights to the study of host-microbiome interactions among a broad range of metazoans, including humans.

Incubation relative humidity induces renal morphological and physiological remodeling in the embryo of the chicken (Gallus gallus domesticus)

The metanephric kidneys of the chicken embryo, along with the chorioallantoic membrane, process water and ions to maintain osmoregulatory homeostasis. We hypothesized that changes in relative humidity (RH) and thus osmotic conditions during embryogenesis would alter the developmental trajectory of embryonic kidney function. White leghorn chicken eggs were incubated at one of 25-30% relative humidity, 55-60% relative humidity, and 85-90% relative humidity. Embryos were sampled at days 10, 12, 14, 16, and 18 to examine embryo and kidney mass, glomerular characteristics, body fluid osmolalities, hematological properties, and whole embryo oxygen consumption. Low and especially high RH elevated mortality, which was reflected in a 10-20% lower embryo mass on D18. Low RH altered several glomerular characteristics by day 18, including increased numbers of glomeruli per kidney, increased glomerular perfusion, and increased total glomerular volume, all indicating potentially increased functional kidney capacity. Hematological variables and plasma and amniotic fluid osmolalities remained within normal physiological values. However, the allantoic, amniotic and cloacal fluids had a significant increase in osmolality at most developmental points sampled. Embryonic oxygen consumption increased relative to control at both low and high relative humidities on Day 18, reflecting the increased metabolic costs of osmotic stress. Major differences in both renal structure and performance associated with changes in incubation humidity occurred after establishment of the metanephric kidney and persisted into late development, and likely into the postnatal period. These data indicate that the avian embryo deserves to be further investigated as a promising model for fetal programming of osmoregulatory function, and renal remodeling during osmotic stress.

Selection Maintains Apparently Degenerate Metabolic Pathways due to Tradeoffs in Using Methylamine for Carbon versus Nitrogen

Microorganisms often encode multiple non-orthologous metabolic modules that catalyze the same reaction. However, little experimental evidence actually demonstrates a selective basis for metabolic degeneracy. Many methylotrophs-microorganisms that grow on reduced single-carbon compounds-like Methylobacterium extorquens AM1 encode two routes for methylamine oxidation: the periplasmic methylamine dehydrogenase (MaDH) and the cytoplasmic N-methylglutamate (NMG) pathway. In Methylobacterium extorquens AM1, MaDH is essential for methylamine growth, but the NMG pathway has no known physiological role. Here, we use experimental evolution of two isolates lacking (or incapable of using) MaDH to uncover the physiological challenges that need to be overcome in order to use the NMG pathway for growth on methylamine as a carbon and energy source. Physiological characterization of the evolved isolates revealed regulatory rewiring to increase expression of the NMG pathway and novel mechanisms to mitigate cytoplasmic ammonia buildup. These adaptations led us to infer and validate environmental conditions under which the NMG pathway is advantageous compared to MaDH. The highly expressed MaDH enables rapid growth on high concentrations of methylamine as the primary carbon and energy substrate, whereas the energetically expensive NMG pathway plays a pivotal role during growth with methylamine as the sole nitrogen source, which we demonstrate is especially true under limiting concentrations (<1 mM). Tradeoffs between cellular localization and ammonium toxicity lead to selection for this apparent degeneracy as it is beneficial to facultative methylotrophs that have to switch between using methylamine as a carbon and energy source or just a nitrogen source.

Integrative Physiology of Fasting

Extended bouts of fasting are ingrained in the ecology of many organisms, characterizing aspects of reproduction, development, hibernation, estivation, migration, and infrequent feeding habits. The challenge of long fasting episodes is the need to maintain physiological homeostasis while relying solely on endogenous resources. To meet that challenge, animals utilize an integrated repertoire of behavioral, physiological, and biochemical responses that reduce metabolic rates, maintain tissue structure and function, and thus enhance survival. We have synthesized in this review the integrative physiological, morphological, and biochemical responses, and their stages, that characterize natural fasting bouts. Underlying the capacity to survive extended fasts are behaviors and mechanisms that reduce metabolic expenditure and shift the dependency to lipid utilization. Hormonal regulation and immune capacity are altered by fasting; hormones that trigger digestion, elevate metabolism, and support immune performance become depressed, whereas hormones that enhance the utilization of endogenous substrates are elevated. The negative energy budget that accompanies fasting leads to the loss of body mass as fat stores are depleted and tissues undergo atrophy (i.e., loss of mass). Absolute rates of body mass loss scale allometrically among vertebrates. Tissues and organs vary in the degree of atrophy and downregulation of function, depending on the degree to which they are used during the fast. Fasting affects the population dynamics and activities of the gut microbiota, an interplay that impacts the host's fasting biology. Fasting-induced gene expression programs underlie the broad spectrum of integrated physiological mechanisms responsible for an animal's ability to survive long episodes of natural fasting.

Molecular characterization, transcriptional activity and nutritional regulation of peroxisome proliferator activated receptor gamma in Nile tilapia (Oreochromis niloticus)

Peroxisome proliferator activated receptor gamma (PPARγ) is a master regulator in lipid metabolism and widely exists in vertebrates. However, the molecular structure and transcriptional activity of PPARγ in fish are still unclear. This study cloned PPARγ from Nile tilapia (Oreochromis niloticus) referred as NtPPARγ and transfected the NtPPARγ plasmids into HEK-293 cells to explore its mechanism of transcriptional regulation in fish. The expression of NtPPARγ was compared in fed and fasted fish. Two transcripts of NtPPARγ varied at the 5'-untranslated region and the DNA binding domain was highly conserved. Thirty-nine amino acid residues in the ligand binding domain in Nile tilapia were different from those in human. Two transcripts showed different expression profiles in 11 tissues, but both were highly expressed in liver, intestine and kidney. The transcriptional activity assay showed that NtPPARγ collaborates with retinoid X-receptor α (NtRXRα) to regulate the expression of Nile tilapia fatty acid binding protein 4 (FABP4), the compartment of which have been identified as the target gene of PPARγ in human. In the fish fasting trial, the mRNA expression of NtPPARγ1 and NtPPARγ2 in intestine and liver at 3h post-feeding (HPF) was lower than those at 8 HPF, 24 HPF and in fish fasted for 36h, but was relatively stable in kidney among different feeding treatments. In conclusion, the DNA binding domain in PPARγ was highly conserved, while the ligand binding domain was moderately conserved. In Nile tilapia, the PPARγ collaborates with RXRα to perform transcriptional regulation of FABP4 at least in vitro. The plasmid system established in this study along with a cell line from Nile tilapia will be useful tools for the further functional study of PPARγ in fish.

Evolution of urea transporters in vertebrates: adaptation to urea's multiple roles and metabolic sources

In the two decades since the first cloning of the mammalian kidney urea transporter (UT-A), UT genes have been identified in a plethora of organisms, ranging from single-celled bacteria to metazoans. In this review, focusing mainly on vertebrates, we first reiterate the multiple catabolic and anabolic pathways that produce urea, then we reconstruct the phylogenetic history of UTs, and finally we examine the tissue distribution of UTs in selected vertebrate species. Our analysis reveals that from an ancestral UT, three homologues evolved in piscine lineages (UT-A, UT-C and UT-D), followed by a subsequent reduction to a single UT-A in lobe-finned fish and amphibians. A later internal tandem duplication of UT-A occurred in the amniote lineage (UT-A1), followed by a second tandem duplication in mammals to give rise to UT-B. While the expected UT expression is evident in excretory and osmoregulatory tissues in ureotelic taxa, UTs are also expressed ubiquitously in non-ureotelic taxa, and in tissues without a complete ornithine-urea cycle (OUC). We posit that non-OUC production of urea from arginine by arginase, an important pathway to generate ornithine for synthesis of molecules such as polyamines for highly proliferative tissues (e.g. testis, embryos), and neurotransmitters such as glutamate for neural tissues, is an important evolutionary driving force for the expression of UTs in these taxa and tissues.

Aldehyde dehydrogenase homologous folate enzymes: Evolutionary switch between cytoplasmic and mitochondrial localization

Cytosolic and mitochondrial 10-formyltetrahydrofolate dehydrogenases are products of separate genes in vertebrates but only one such gene is present in invertebrates. There is a significant degree of sequence similarity between the two enzymes due to an apparent origin of the gene for the mitochondrial enzyme (ALDH1L2) from the duplication of the gene for the cytosolic enzyme (ALDH1L1). The primordial ALDH1L gene originated from a natural fusion of three unrelated genes, one of which was an aldehyde dehydrogenase. Such structural organization defined the catalytic mechanism of these enzymes, which is similar to that of aldehyde dehydrogenases. Here we report the analysis of ALDH1L1 and ALDH1L2 genes from different species and their phylogeny and evolution. We also performed sequence and structure comparison of ALDH1L enzymes possessing aldehyde dehydrogenase catalysis to those lacking this feature in an attempt to explain mechanistic differences between cytoplasmic ALDH1L1 and mitochondrial ALDH1L2 enzymes and to better understand their functional roles.

Animal-microbial symbioses in changing environments

The environments in which animals have evolved and live have profound effects on all aspects of their biology. Predictable rhythmic changes in the physical environment are arguably among the most important forces shaping the evolution of behavior and physiology of animals, and to anticipate and prepare for these predictable changes, animals have evolved biological clocks. Unpredictable changes in the physical environment have important impacts on animal biology as well. The ability of animals to cope with and survive unpredictable perturbations depends on phenotypic plasticity and/or microevolution. From the time metazoans first evolved from their protistan ancestors they have lived in close association with a diverse array of microbes that have influenced, in some way, all aspects of the evolution of animal structure, function and behavior. Yet, few studies have addressed whether daily or seasonal rhythms may affect, or be affected by, an animal's microbial symbionts. This survey highlights how biologists interested in the ecological and evolutionary physiology of animals whose lifestyles are influenced by environmental cycles may benefit from considering whether symbiotic microbes have shaped the features they study.

Elements in the Development of a Production Process for Modified Vaccinia Virus Ankara

The production of several viral vaccines depends on chicken embryo fibroblasts or embryonated chicken eggs. To replace this logistically demanding substrate, we created continuous anatine suspension cell lines (CR and CR.pIX), developed chemically-defined media, and established production processes for different vaccine viruses. One of the processes investigated in greater detail was developed for modified vaccinia virus Ankara (MVA). MVA is highly attenuated for human recipients and an efficient vector for reactogenic expression of foreign genes. Because direct cell-to-cell spread is one important mechanism for vaccinia virus replication, cultivation of MVA in bioreactors is facilitated if cell aggregates are induced after infection. This dependency may be the mechanism behind our observation that a novel viral genotype (MVA-CR) accumulates with serial passage in suspension cultures. Sequencing of a major part of the genomic DNA of the new strain revealed point mutations in three genes. We hypothesize that these changes confer an advantage because they may allow a greater fraction of MVA-CR viruses to escape the host cells for infection of distant targets. Production and purification of MVA-based vaccines may be simplified by this combination of designed avian cell line, chemically defined media and the novel virus strain.

Isotope incorporation in broad-snouted caimans (crocodilians)

The trophic ecology and migration of vertebrate species have been increasingly studied using stable isotope analysis. However, this approach requires knowledge on how dietary isotopic values are reflected in consumers' tissues. To date, this information has only been obtained for a handful of ectotherms; in particular, little is known about crocodilians. In this study, diet-tissue discrimination factors (DTDFs) and carbon and nitrogen stable isotope turnover rates were estimated for plasma, red blood cells (RBCs), and muscle obtained from broad-snouted caimans (Caiman latirostris). Individuals were fed two different control diets for 189 days. DTDFs for δ¹⁵N (Δ¹⁵N) and δ¹³C (Δ¹³C) ranged from −2.24‰ to 0.39‰ and from −0.52‰ to 1.06‰, respectively. Isotope turnover rates in tissues, expressed as half-lives, ranged from 11 to 71 days, with plasma<muscle<RBCs. Δ¹⁵N was found to be particularly small, even when compared to values found for other ectotherms, a result that may be linked to the unique excretion physiology of crocodilians. These stable isotope incorporation data should help inform future interpretations of isotopic values obtained in the field for this taxon.

High NaCl- and urea-induced posttranslational modifications that increase glycerophosphocholine by inhibiting GDPD5 phosphodiesterase

Glycerophosphocholine (GPC) is high in cells of the renal inner medulla where high interstitial NaCl and urea power concentration of the urine. GPC protects inner medullary cells against the perturbing effects of high NaCl and urea by stabilizing intracellular macromolecules. Degradation of GPC is catalyzed by the glycerophosphocholine phosphodiesterase activity of glycerophosphodiester phosphodiesterase domain containing 5 (GDPD5). We previously found that inhibitory posttranslational modification (PTM) of GDPD5 contributes to high NaCl- and urea-induced increase of GPC. The purpose of the present studies was to identify the PTM(s). We find at least three such PTMs in HEK293 cells: (i) Formation of a disulfide bond between C25 and C571. High NaCl and high urea increase reactive oxygen species (ROS). The ROS increase disulfide bonding between GDPD5-C25 and -C571, which inhibits GDPD5 activity, as supported by the findings that the antioxidant N-acetylcysteine prevents high NaCl- and urea-induced inhibition of GDPD5; GDPD5-C25S/C571S mutation or over expression of peroxiredoxin increases GDPD5 activity; H2O2 inhibits activity of wild type GDPD5, but not of GDPD5-C25S/C571S; and peroxiredoxin is relatively low in the renal inner medulla where GPC is high. (ii) Dephosphorylation of GDPD5-T587. GDPD5 threonine 587 is constitutively phosphorylated. High NaCl and high urea dephosphorylate GDPD5-T587. Mutation of GDPD5-T587 to alanine, which cannot be phosphorylated, decreases GPC-PDE activity of GDPD5. (iii) Alteration at an unknown site mediated by CDK1. Inhibition of CDK1 protein kinase reduces GDE-PDE activity of GDPD5 without altering phosphorylation at T587, and CDK1/5 inhibitor reduces activity of GDPD5- C25S/C571S-T587A.

Fish welfare and genomics

There is a considerable public and scientific debate concerning welfare of fish in aquaculture. In this review, we will consider fish welfare as an integration of physiological, behavioral, and cognitive/emotional responses, all of which are essentially adaptative responses to stressful situations. An overview of fish welfare in this context suggests that understanding will rely on knowledge of all components of allostatic responses to stress and environmental perturbations. The development of genomic technologies provides new approaches to this task, exemplified by how genome-wide analysis of genetic structures and corresponding expression patterns can lead to the discovery of new aspects of adaptative responses. We will illustrate how the genomic approach may give rise to new biomarkers for fish welfare and also increase our understanding of the interaction between physiological, behavioral, and emotional responses. In a first part, we present data on expression of candidate genes selected a priori. This is a common avenue to develop molecular biomarkers capable of diagnosing a stress condition at its earliest onset, in order to allow quick corrective intervention in an aquaculture setting. However, most of these studies address isolated physiological functions and stress responses that may not be truly indicative of animal welfare, and there is only rudimentary understanding of genes related to possible cognitive and emotional responses in fish. We also present an overview on transcriptomic analysis related to the effect of aquaculture stressors, environmental changes (temperature, salinity, hypoxia), or concerning specific behavioral patterns. These studies illustrate the potential of genomic approaches to characterize the complexity of the molecular mechanisms which underlies not only physiological but also behavioral responses in relation to fish welfare. Thirdly, we address proteomic studies on biological responses to stressors such as salinity change and hypoxia. We will also consider proteomic studies developed in mammals in relation to anxiety and depressive status which may lead to new potential candidates in fish. Finally, in the conclusion, we will suggest new developments to facilitate an integrated view of fish welfare. This includes use of laser microdissection in the transcriptomic/proteomic studies, development of meta-analysis methods for extracting information from genomic data sets, and implementation of technological advances for high-throughput proteomic studies. Development of these new approaches should be as productive for our understanding of the biological processes underlying fish welfare as it has been for the progress of pathophysiological research.

Crystal structure of urea carboxylase provides insights into the carboxyltransfer reaction

Urea carboxylase (UC) is conserved in many bacteria, algae, and fungi and catalyzes the conversion of urea to allophanate, an essential step in the utilization of urea as a nitrogen source in these organisms. UC belongs to the biotin-dependent carboxylase superfamily and shares the biotin carboxylase (BC) and biotin carboxyl carrier protein (BCCP) domains with these other enzymes, but its carboxyltransferase (CT) domain is distinct. Currently, there is no information on the molecular basis of catalysis by UC. We report here the crystal structure of the Kluyveromyces lactis UC and biochemical studies to assess the structural information. Structural and sequence analyses indicate the CT domain of UC belongs to a large family of proteins with diverse functions, including the Bacillus subtilis KipA-KipI complex, which has important functions in sporulation regulation. A structure of the KipA-KipI complex is not currently available, and our structure provides a framework to understand the function of this complex. Most interestingly, in the structure the CT domain interacts with the BCCP domain, with biotin and a urea molecule bound at its active site. This structural information and our follow-up biochemical experiments provided molecular insights into the UC carboxyltransfer reaction. Several structural elements important for the UC carboxyltransfer reaction are found in other biotin-dependent carboxylases and might be conserved within this family, and our data could shed light on the mechanism of catalysis of these enzymes.

An aminotransferase branch point connects purine catabolism to amino acid recycling

Although amino acids are known precursors of purines, a pathway for the direct recycling of amino acids from purines has never been described at the molecular level. We provide NMR and crystallographic evidence that the PucG protein from Bacillus subtilis catalyzes the transamination between an unstable intermediate ((S)-ureidoglycine) and the end product of purine catabolism (glyoxylate) to yield oxalurate and glycine. This activity enables soil and gut bacteria to use the animal purine waste as a source of carbon and nitrogen. The reaction catalyzed by (S)-ureidoglycine-glyoxylate aminotransferase (UGXT) illustrates a transamination sequence in which the same substrate provides both the amino group donor and, via its spontaneous decay, the amino group acceptor. Structural comparison and mutational analysis suggest a molecular rationale for the functional divergence between UGXT and peroxisomal alanine-glyoxylate aminotransferase, a fundamental enzyme for glyoxylate detoxification in humans.

Differential ammonia metabolism in Aedes aegypti fat body and midgut tissues

In order to understand at the tissue level how Aedes aegypti copes with toxic ammonia concentrations that result from the rapid metabolism of blood meal proteins, we investigated the incorporation of (15)N from (15)NH(4)Cl into amino acids using an in vitro tissue culture system. Fat body or midgut tissues from female mosquitoes were incubated in an Aedes saline solution supplemented with glucose and (15)NH(4)Cl for 10-40min. The media were then mixed with deuterium-labeled amino acids, dried and derivatized. The (15)N-labeled and unlabeled amino acids in each sample were quantified by mass spectrometry techniques. The results demonstrate that both tissues efficiently incorporate ammonia into amino acids, however, the specific metabolic pathways are distinct. In the fat body, the (15)N from (15)NH(4)Cl is first incorporated into the amide side chain of Gln and then into the amino group of Gln, Glu, Ala and Pro. This process mainly occurs via the glutamine synthetase (GS) and glutamate synthase (GltS) pathway. In contrast, (15)N in midgut is first incorporated into the amino group of Glu and Ala, and then into the amide side chain of Gln. Interestingly, our data show that the GS/GltS pathway is not functional in the midgut. Instead, midgut cells detoxify ammonia by glutamate dehydrogenase, alanine aminotransferase and GS. These data provide new insights into ammonia metabolism in A. aegypti mosquitoes.