Development-specific transcriptomic profiling suggests new mechanisms for anoxic survival in the ventricle of overwintering turtles.

Oxygen deprivation swiftly damages tissues in most animals, yet some species show remarkable abilities to tolerate little or even no oxygen. Painted turtles exhibit a development-dependent tolerance that allows adults to survive anoxia approximately four times longer than hatchlings: adults survive ∼170 days and hatchlings survive ∼40 days at 3°C. We hypothesized that this difference is related to development-dependent differences in ventricular gene expression. Using a comparative ontogenetic approach, we examined whole transcriptomic changes before, during and 5 days after a 20-day bout of anoxic submergence at 3°C. Ontogeny accounted for more gene expression differences than treatment (anoxia or recovery): 1175 versus 237 genes, respectively. Of the 237 differences, 93 could confer protection against anoxia and reperfusion injury, 68 could be injurious and 20 may be constitutively protective. Most striking during anoxia was the main expression pattern of all 76 annotated ribosomal protein (R-protein) mRNAs, which decreased in anoxia-tolerant adults, but increased in anoxia-sensitive hatchlings, suggesting adult-specific regulation of translational suppression. These genes, along with 60 others that decreased their levels in adults and either increased or remained unchanged in hatchlings, implicate antagonistic pleiotropy as a mechanism to resolve the long-standing question about why hatchling painted turtles overwinter in terrestrial nests, rather than emerge and overwinter in water during their first year. In summary, developmental differences in the transcriptome of the turtle ventricle revealed potentially protective mechanisms that contribute to extraordinary adult-specific anoxia tolerance, and provide a unique perspective on differences between the anoxia-induced molecular responses of anoxia-tolerant and anoxia-sensitive phenotypes within a species.

Heterogeneous bioapatite carbonation in western painted turtles is unchanged after anoxia.

Adsorbed and structurally incorporated carbonate in bioapatite, the primary mineral phase of bone, is observed across vertebrates, typically at 2-8 wt%, and supports critical physiological and biochemical functions. Several turtle species contain elevated bone-associated carbonate, a property linked to pH buffering and overwintering survival. Prior studies of turtle bone utilized bulk analyses, which do not provide spatial resolution of carbonate. Using Raman spectroscopy, the goals of this study were to: (1) quantify and spatially resolve carbonate heterogeneity within the turtle shell; (2) determine if cortical and trabecular bone contain distinct carbonate concentrations; and (3) assess if simulated overwintering conditions result in decreased bioapatite carbonation. Here, we demonstrate the potential for Raman spectroscopic analysis to spatially resolve bioapatite carbonation, using the western painted turtle as a model species. Carbonate concentration was highly variable within cortical and trabecular bone, based on calibrated Raman spot analyses and mapping, suggesting heterogeneous carbonate distribution among crystallites. Mean carbonate concentration did not significantly differ between cortical and trabecular bone, which indicates random distribution of crystallites with elevated and depleted carbonate. Carbonate concentrations (range: 5-22 wt%) were not significantly different in overwintering and control animals, deviating from previous bulk analyses. In reconciling bulk and Raman analyses, two hypotheses explain how overwintering turtles potentially access carbonate: (1) mobilization of mineral-associated, surface components of bone crystallites; and (2) selective, dispersed crystallite dissolution. Elevated bioapatite carbonate in the western painted turtle, averaging 11.8 wt%, represents the highest carbonation observed in vertebrates, and is one physiological trait that facilitates overwintering survival.

Changes in the material properties of the shell during simulated aquatic hibernation in the anoxia-tolerant painted turtle.

Western painted turtles (Chrysemys picta bellii) tolerate anoxic submergence longer than any other tetrapod, surviving more than 170 days at 3°C. This ability is due, in part, to the shell and skeleton simultaneously releasing calcium and magnesium carbonates, and sequestering lactate and H+ to prevent lethal decreases in body fluid pH. We evaluated the effects of anoxic submergence at 3°C on various material properties of painted turtle bone after 60, 130 and 167-170 days, and compared them with those of normoxic turtles held at the same temperature for the same time periods. To assess changes in the mechanical properties, beams (4×25 mm) were milled from the plastron and broken in a three-point flexural test. Bone mineral density, CO2 concentration (a measure of total bone HCO3-/CO32-) and elemental composition were measured using microcomputed tomography, HCO3-/CO32- titration and inductively coupled plasma mass spectrometry (ICP-MS), respectively. Tissue mineral density of the sampled bone beams was not significantly altered by 167-170 days of aquatic overwintering in anoxic or normoxic water, but bone CO2 and Mg were depleted in anoxic compared with normoxic turtles. At this time point, the plastron beams from anoxic turtles yielded at stresses that were significantly smaller and strains that were significantly greater than the plastron beams of normoxic turtles. When data from anoxic and normoxic turtles were pooled, plastron beams had a diminished elastic modulus after 167-170 days compared with those of control turtles sampled on day 1, indicating an effect of prolonged housing of the turtles in 3°C water without access to basking sites. There were no changes in the mechanical properties of the plastron beams at any of the earlier time points in either group. We conclude that anoxic hibernation can weaken the painted turtle's plastron, but likely only after durations that exceed what it might naturally experience. The duration of aquatic overwintering, regardless of oxygenation state, is likely to be an important factor determining the mechanical properties of the turtle shell during spring emergence.

Long-term effects of buried vertebrate carcasses on soil biogeochemistry in the Northern Great Plains.

Decomposing vertebrates impact ecosystems by stimulating animal, insect, and microbial scavengers, perturbing biogeochemical cycles, and transferring elements back to the environment. Most studies exploring the impacts of vertebrate decomposition focus on surface decay scenarios over timescales of days to years. Accordingly, our knowledge of ecosystem impacts of vertebrate decomposition in burial contexts and over longer time scales is limited. In 2000, six animal carcasses were buried in a shallow grave (<1.0 m) and allowed to decompose naturally until partial excavation in 2021, enabling evaluation of long-term soil biogeochemical responses to decomposing vertebrates. Soils were sampled along three vertical transects from the surface to the bone-bearing layer (~40 cm depth) and below. Comparison of the physical and chemical properties of the grave and control soils from equivalent depths indicate significant perturbations even 21 years after burial. Notably, soil pH was significantly more acidic in grave soils (p = 0.0296), and conductivity was significantly elevated (p = 0.0009). Grave soils were significantly enriched with respect to nitrogen stable isotopes, exhibiting δ15N values of 10.48 ± 3.6‰, which is ~5‰ greater than controls. Carbon and nitrogen content was also disrupted in the burial, with five times more nitrogen in the bone-bearing layer and almost double the carbon. Water and acid-based extractions of soils revealed significant differences between grave and control soils, driven largely by calcium, phosphorus (P), magnesium, and iron concentrations. P concentrations in acid extracts were significantly enriched at the bone-bearing layer, suggesting release of P from the bones. This study demonstrates that decomposition may result in long-lived impacts to burial environments and soil biogeochemistry, even after soft tissues decay. While not typically considered in ecosystem models, buried remains contribute to soils for decades or longer, and soil biogeochemistry serves a critical role in facilitating or preventing the long-term preservation of bone.

Experimental dissolution of fossil bone under variable pH conditions.

Fossils exposed at the surface are an integral component of the paleontologic record and provide an archive of past life. However, it is widely known that fossils are not stable indefinitely upon exposure to surface conditions such as physical, chemical, and biological processes, and this last phase of taphonomy is poorly understood. Studies regarding the longevity of fossils subject to weathering, such as acidic precipitation, are absent in the literature. The goal of this study was to experimentally determine vertebrate fossil dissolution rates under variable pH conditions in a controlled laboratory setting. It was hypothesized that fossils would dissolve within acidic solutions and do so at an increasing rate when exposed to increasingly acidic solutions. The experiments were conducted on three fossil vertebrae in triplicate in closed reaction vessels at pH 4, 5, and 6. The fossils were completely submerged for 21 days in a tap water solution with the pH adjusted using 0.1N hydrochloric acid (HCl). Fossil dissolution was quantified by changes to: (1) fossil mass; (2) elemental chemistry of water and fossils with inductively coupled plasma mass spectrometry (ICP-MS); (3) fossil mineralogy with X-ray diffraction (XRD); and (4) histologic structures with thin section analyses. All fossils exhibited mass loss, which increased with decreasing pH conditions, and was greatest under pH 4 (477 to 803 mg loss). The elemental analyses with ICP-MS indicated an increase of both calcium (maximum increase of 315 ppm) and phosphorus (increase of 18 ppm) in aqueous solutions with increasing pH and a loss of those same elements from the fossils (maximum loss of 10 ppm Ca and 6 ppm P). XRD revealed loss of gypsum in all post-dissolution samples. Taken together, the results of ICP-MS and XRD suggest dissolution of the primary mineral phases, including hydroxylapatite, and secondary phases, particularly calcite and gypsum, resulting in an estimated mass loss at pH 4 of 23 to 28 mg per day. Thin section analysis showed degradation of both cortical and trabecular bone in all post-dissolution images, demonstrating physical changes to the fossils as a result of water-rock interactions. These findings constitute the first quantitative analysis of fossil dissolution rates and provide insights into this last stage of taphonomy, addressing a largely understudied potential bias in the vertebrate fossil record.

Postmortem Skeletal Microbial Community Composition and Function in Buried Human Remains.

Bones and teeth can provide a lasting resource to identify human remains following decomposition. Bone can support dynamic communities of micro- and macroscopic scavengers and incidental taxa, which influence the preservation of bone over time. Previously we identified key microbial taxa associated with survivability of DNA in bones of surface-decomposed human remains, observing high intra- and interindividual variation. Here we characterized the postmortem bone microbiome of skeletal remains in a multi-individual burial to better understand subsurface bone colonization and preservation. To understand microbial community origins and assembly, 16S rRNA amplicon sequences from 256 bone and 27 soil samples were compared to bone from individuals who decomposed on the ground surface, and human gut sequences from the American Gut Project. Untargeted metabolomics was applied to a subset of 41 bone samples from buried remains to examine potential microbe-metabolite interactions and infer differences related to community functionality. Results show that postmortem bone microbial communities are distinct from those of the oxic surface soils and the human gut. Microbial communities from surface-deposited bone and shallow buried bone were more similar to those from soils, while bones recovered from saturated areas deeper in the grave showed increased similarity with human gut samples with higher representation of anaerobic taxa, suggesting that the depositional environment affected the established bone microbiome. Correlations between metabolites and microbes indicate that phosphate solubilization is likely an important mechanism of microbially mediated skeletal degradation. This research expands our knowledge of microbial bone colonizers, including colonizers important in a burial environment. IMPORTANCE Understanding the microbes that colonize and degrade bone has important implications for preservation of skeletal elements and identification of unknown human remains. Current research on the postmortem bone microbiome is limited and largely focuses on archaeological or marine contexts. Our research expands our understanding of bone microbiomes in buried remains by characterizing the taxonomic and metabolic diversity of microbes that are colonizing bone after a 4-year postmortem burial interval and examines the potential impact of microbial colonization on human skeletal DNA preservation. Our results indicate that the postmortem bone microbiome is distinct from the human gut and soil. Evidence from combined metabolomic and amplicon sequencing analysis suggests that Pseudomonas and phosphate solubilization likely play a role in skeletal degradation. This work provides important insight into the types and activities of microbes controlling the preservation of buried skeletal remains.

Characterizing the postmortem human bone microbiome from surface-decomposed remains.

Microbial colonization of bone is an important mechanism of postmortem skeletal degradation. However, the types and distributions of bone and tooth colonizing microbes are not well characterized. It is unknown if microbial communities vary in abundance or composition between bone element types, which could help explain differences in human DNA preservation. The goals of the present study were to (1) identify the types of microbes capable of colonizing different human bone types and (2) relate microbial abundances, diversity, and community composition to bone type and human DNA preservation. DNA extracts from 165 bone and tooth samples from three skeletonized individuals were assessed for bacterial loading and microbial community composition and structure. Random forest models were applied to predict operational taxonomic units (OTUs) associated with human DNA concentration. Dominant bacterial bone colonizers were from the phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Planctomycetes. Eukaryotic bone colonizers were from Ascomycota, Apicomplexa, Annelida, Basidiomycota, and Ciliophora. Bacterial loading was not a significant predictor of human DNA concentration in two out of three individuals. Random forest models were minimally successful in identifying microbes related to human DNA concentration, which were complicated by high variability in community structure between individuals and body regions. This work expands on our understanding of the types of microbes capable of colonizing the postmortem human skeleton and potentially contributing to human skeletal DNA degradation.

Changes to vertebrate tissue stable isotope (δ15N) composition during decomposition.

During carcass decomposition, tissues undergo biochemical changes: Cells autolyze, enteric microbes ferment cellular products, and tissues degrade. Ultimately, decomposition fluids are released as an ephemeral nitrogen (N) and carbon source to the surrounding environment. However, decomposition fluids are δ15N-enriched relative to body tissues, leading to a disconnect between starting tissue composition and ending fluid composition. It remains largely unknown when or if tissues exhibit δ15N enrichment postmortem despite the importance of tissue stable isotopes to ecologists. To test our hypothesis that tissues would become progressively δ15N-enriched during decay, soft tissues and bone were collected from beaver carcasses at five time points. All soft tissues, including muscle, were significantly δ15N-enriched compared to fresh tissues, but were not as enriched as decomposition fluids. Tissue breakdown is initially dominated by anaerobic autolysis and later by microbe and insect infiltration, and partly explains decay fluid isotopic enrichment. We speculate that after rupture, preferential volatilization of δ15N-depleted compounds (especially ammonia) contributes to further enrichment. These results constrain the timing, rate, and potential mechanisms driving carcass isotopic enrichment during decay, and suggest that found carcasses (e.g., road kill) should be used with caution for inferring trophic ecology as decay can result in significant postmortem δ15N enrichment.

Spatial impacts of a multi-individual grave on microbial and microfaunal communities and soil biogeochemistry.

Decomposing vertebrates, including humans, result in pronounced changes in surrounding soil biogeochemistry, particularly nitrogen (N) and carbon (C) availability, and alter soil micro- and macrofauna. However, the impacts of subsurface human decomposition, where oxygen becomes limited and microbial biomass is generally lower, are far less understood. The goals of this study were to evaluate the impact of human decomposition in a multi-individual, shallow (~70 cm depth) grave on soil biogeochemistry and soil microbial and nematode communities. Three individuals were interred and allowed to decay for four years. Soils were collected from two depths (0‒5 and 30‒35 cm) along linear transects radiating from the grave as well as from within and below (85‒90 cm depth) the grave during excavation to assess how decomposition affects soil properties. Along radiating surface transects, several extracellular enzymes rates and nematode richness increased with increasing distance from the grave, and likely reflect physical site disruption due to grave excavation and infill. There was no evidence of carcass-sourced C and N lateral migration from the grave, at least at 30‒35 cm depth. Within the grave, soils exhibited significant N-enrichment (e.g., ammonium, dissolved organic N), elevated electrical conductivity, and elevated respiration rates with depth. Soil biogeochemistry within the grave, particularly in the middle (30‒35 cm) and base (70‒75 cm depth), was significantly altered by human decomposition. Mean microbial gene abundances changed with depth in the grave, demonstrating increased microbial presence in response to ongoing decomposition. Human-associated Bacteroides were only detected at the base of the grave where anoxic conditions prevailed. Nematode community abundance and richness were reduced at 70‒75 cm and not detectable below 85‒90 cm. Further, we identified certain Plectus spp. as potential indicators of enrichment due to decomposition. Here we demonstrate that human decomposition influences soil biogeochemistry, microbes, and microfauna up to four years after burial.

The Good, the Bad, and the Unknown: Microbial Symbioses of the American Alligator.

Vertebrates coexist with microorganisms in diverse symbiotic associations that range from beneficial to detrimental to the host. Most research has aimed at deciphering the nature of the composite microbial assemblage's genome, or microbiome, from the gastrointestinal (GI) tract and skin of mammals (i.e., humans). In mammals, the GI tract's microbiome aids digestion, enhances uptake of nutrients, and prevents the establishment of pathogenic microorganisms. However, because the GI tract microbiome of the American alligator (Alligator mississippiensis) is distinct from that of all other vertebrates studied to date, being comprised of Fusobacteria in the lower GI tract with lesser abundances of Firmicutes, Proteobacteria, and Bacteroidetes, the function of these assemblages is largely unknown. This review provides a synthesis of our current understanding of the composition of alligators' microbiomes, highlights the potential role of microbiome members in alligators' health (the good), and presents a brief summary of microorganisms detrimental to alligators' health (the bad) including Salmonella spp. and others. Microbial assemblages of the GI tract have co-evolved with their vertebrate host over geologic time, which means that evolutionary hypotheses can be tested using information about the microbiome. For reptiles and amphibians, the number of taxa studied at present is limited, thereby restricting evolutionary insights. Nevertheless, we present a compilation of our current understanding of reptiles' and amphibians' microbiomes, and highlight future avenues of research (the unknown). As in humans, composition of microbiome assemblages provides a promising tool for assessing hosts' health or disease. By further exploring present-day associations between symbiotic microorganisms in the microbiomes of reptiles and amphibians, we can better identify good (beneficial) and bad (detrimental) microorganisms, and unravel the evolutionary history of the acquisition of microbiomes by these poorly-studied vertebrates.

Transcriptomic Responses of the Heart and Brain to Anoxia in the Western Painted Turtle.

Painted turtles are the most anoxia-tolerant tetrapods known, capable of surviving without oxygen for more than four months at 3°C and 30 hours at 20°C. To investigate the transcriptomic basis of this ability, we used RNA-seq to quantify mRNA expression in the painted turtle ventricle and telencephalon after 24 hours of anoxia at 19°C. Reads were obtained from 22,174 different genes, 13,236 of which were compared statistically between treatments for each tissue. Total tissue RNA contents decreased by 16% in telencephalon and 53% in ventricle. The telencephalon and ventricle showed ≥ 2x expression (increased expression) in 19 and 23 genes, respectively, while only four genes in ventricle showed ≤ 0.5x changes (decreased expression). When treatment effects were compared between anoxic and normoxic conditions in the two tissue types, 31 genes were increased (≥ 2x change) and 2 were decreased (≤ 0.5x change). Most of the effected genes were immediate early genes and transcription factors that regulate cellular growth and development; changes that would seem to promote transcriptional, translational, and metabolic arrest. No genes related to ion channels, synaptic transmission, cardiac contractility or excitation-contraction coupling changed. The generalized expression pattern in telencephalon and across tissues, but not in ventricle, correlated with the predicted metabolic cost of transcription, with the shortest genes and those with the fewest exons showing the largest increases in expression.

The alligator gut microbiome and implications for archosaur symbioses.

Among vertebrate gastrointestinal microbiome studies, complete representation of taxa is limited, particularly among reptiles. Here, we provide evidence for previously unrecognized host-microbiome associations along the gastrointestinal tract from the American alligator, a crown archosaur with shared ancestry to extinct taxa, including dinosaurs. Microbiome compositional variations reveal that the digestive system consists of multiple, longitudinally heterogeneous microbiomes that strongly correlate to specific gastrointestinal tract organs, regardless of rearing histories or feeding status. A core alligator gut microbiome comprised of Fusobacteria, but depleted in Bacteroidetes and Proteobacteria common to mammalians, is compositionally unique from other vertebrate gut microbiomes, including other reptiles, fish, and herbivorous and carnivorous mammals. As such, modern alligator gut microbiomes advance our understanding of archosaur gut microbiome evolution, particularly if conserved host ecology has retained archosaur-specific symbioses over geologic time.