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Conservation efforts for endangered sea turtle species, such as Kemp’s ridley turtles Lepidochelys kempii and green turtles Chelonia mydas, may benefit from information on the microbial communities that contribute to host health. Previous studies examining host-associated microbiomes of these species have been limited in geographic region, life stage, and/or health. Here, we characterized the microbiome of the oral cavity and cloaca from wild-captured Kemp’s ridley and green turtles off the west coast of Florida, USA, by using Illumina sequencing to analyze the 16S rRNA gene. Microbial communities were distinct between body sites as well as between turtle species, suggesting that the turtle species is more important than the local environment in determining the microbiome of sea turtles. We identified the core microbiome for each species at each body site and determined that there were very few bacteria shared among the oral samples of both species, and no taxa co-occurred in the cloaca samples among both species. The core microbiome of the green turtle cloaca was primarily from the order Clostridiales, which plays an important role in digestion for other herbivorous species. Due to high prevalence of fibropapillomatosis in the green turtles (90%), we also investigated the correlation between the microbiome and the severity of fibropapillomatosis, and we identified changes in beta diversity associated with the total number of tumors. This study provides the first glimpse of the microbiome in 2 sympatric species of sea turtle and sheds an important species-specific light on the microbiome of these endangered species.

Simple Summary A tracheal lavage is commonly used to characterize the microbes that may be causing pneumonia in sea turtles, typically by culture-dependent methods. In this study, we characterized the tracheal lavage microbiome through culture-independent methods and compared the resulting sequence data to conventional cultures, the degree of radiographic lung abnormalities, and pathogens of sea turtles as previously reported in the literature. This study also evaluates the microbial communities at different sections of the respiratory tract from deceased sea turtles. We found that radiographic lung abnormalities do not correlate with the tracheal lavage microbiome, tracheal lavage cultures under-represent the microbial community as determined by culture-independent methods, many previously reported sea turtle pathogens are present in low abundance of the tracheal lavage microbiome, and tracheal lavages are not representative of other sections of the respiratory tract. Abstract Respiratory disease is a common cause of morbidity and mortality in sea turtles, including the Kemp’s ridley sea turtle (Lepidochelys kempii). Although culture-dependent methods are typically used to characterize microbes associated with pneumonia and to determine treatment, culture-independent methods can provide a deeper understanding of the respiratory microbial communities and lead to a more accurate diagnosis. In this study, we characterized the tracheal lavage microbiome from cold-stunned Kemp’s ridley sea turtles at three time points during rehabilitation (intake, rehabilitation, and convalescence) by analyzing the 16S rRNA gene collected from tracheal lavage samples. We retrospectively developed a radiographic scoring system to grade the severity of lung abnormalities in these turtles and found no differences in diversity or composition of microbial communities based on radiographic score. We also found that the culture isolates from tracheal lavage samples, as well as other previously reported sea turtle pathogens, were present in variable abundance across sequenced samples. In addition to the tracheal microbial community of live turtles, we characterized microbial communities from other segments of the respiratory tract (glottis, trachea, anterior lung, posterior lung) from deceased turtles. We found a high degree of variability within turtles and a high degree of dissimilarity between different segments of the respiratory tract and the tracheal lavage collected from the same turtle. In summary, we found that the pulmonary microbial community associated with pneumonia in sea turtles is complex and does not correlate well with the microbial community as identified by tracheal lavage. These results underscore the limitations of using tracheal lavage for identification of the causative agents of pneumonia in sea turtles.

Blood was collected from wild captured green and Kemp's ridley turtles off the west coast of Florida, USA. Blood gases and biochemical values were analyzed using a point of care (POC) device in the field. Analytes include pH, partial pressure of carbon dioxide (pCO2), partial pressure of oxygen (pO2), total carbon dioxide (TCO2), bicarbonate (HCO3), base excess (BE), oxygen saturation (sO2), lactate, sodium (Na), potassium (K), chloride (Cl), total carbon dioxide (TCO2), anion gap, ionized calcium, glucose, blood urea nitrogen (BUN), creatinine (Crea), hematocrit (Hct), and hemoglobin (Hb). These are novel data for wild healthy Kemp's ridley turtles, and results for green turtles were generally consistent with past studies of green turtles with exceptions primarily in blood gas values. Ninety percent of the green turtles had fibropapillomatosis (FP), but none of the blood analytes were correlated with disease severity. Only BUN was correlated with weight of green turtles, and there was no correlation between blood parameters and weight of Kemp's ridley turtles. This study provides data that are useful in understanding the physiologic status of sea turtles specific to this region, allowing for comparisons to other populations, life stages, and disease states.

Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors.Here, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host phylogeny, and trophic level/diet. Specifically, external microbiomes are best explained by variations in mean daily temperature range and precipitation seasonality. In contrast, internal microbiomes are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus climate.Internal microbiomes are predominantly associated with top-down effects, while climatic factors are stronger determinants of microbiomes on host external surfaces. Host immunity may act on microbiome diversity through top-down regulation analogous to predators in non-microbial ecosystems. Noting gaps in geographic and host sampling, this combined dataset represents a global baseline available for interrogation by future microbial ecology studies.

BackgroundHost-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors.ResultsHere, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host phylogeny, and trophic level/diet. Specifically, external microbiomes are best explained by variations in mean daily temperature range and precipitation seasonality. In contrast, internal microbiomes are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus climate.ConclusionsInternal microbiomes are predominantly associated with top-down effects, while climatic factors are stronger determinants of microbiomes on host external surfaces. Host immunity may act on microbiome diversity through top-down regulation analogous to predators in non-microbial ecosystems. Noting gaps in geographic and host sampling, this combined dataset represents a global baseline available for interrogation by future microbial ecology studies.

SynopsisMany juvenile Kemp’s ridley (Lepidochelys kempii) and loggerhead (Caretta caretta) turtles strand during fall on the beaches of Cape Cod (MA, USA), with total stranding numbers sometimes exceeding 300 turtles per year. Once rehabilitated, turtles must be released at beaches with appropriate water temperatures, often requiring transportation to southeastern coastal states of the USA. These transportation events (transports) may approach or exceed 24 h in duration. Kemp’s ridley turtles are known to exhibit an adrenal stress response during such transports, but the effect of transport duration has been unclear, and no other sea turtle species has been investigated. To assess whether transport duration and/or species affects physiological reactions to transport, we studied pre- and post-transport physiological measures in Kemp’s ridley and loggerhead turtles transported by ground for

Microbial communities of animals play a role in health and disease, including immunocompromised conditions. In the northeastern United States, cold-stunning events often cause endangered Kemp’s ridley turtles (Lepidochelys kempii) to become stranded on beaches in autumn. These sea turtles are admitted to rehabilitation facilities when rescued alive and are presumed immunocompromised secondary to hypothermia. To better understand the role that microbes play in the health of cold-stunned sea turtles, we characterized the oral and cloacal microbiome from Kemp’s ridley turtles at multiple timepoints during rehabilitation, from admission to pre-release, by using Illumina sequencing to analyze the 16S rRNA gene. Microbial communities were distinct between body sites and among turtles that survived and those that died. We found that clinical parameters such as presence of pneumonia or values for various blood analytes did not correlate with oral or cloacal microbial community composition. We also investigated the effect of antibiotics on the microbiome during rehabilitation and prior to release and found that the type of antibiotic altered the microbial community composition, yet overall taxonomic diversity remained the same. The microbiome of cold-stunned Kemp’s ridley turtles gradually changed through the course of rehabilitation with environment, antibiotics, and disease status all playing a role in those changes and ultimately the release status of the turtles.

Cold-stunned loggerhead sea turtles (Caretta caretta) strand annually in the northeastern United States and are admitted to rehabilitation facilities when rescued alive. Hematologic and plasma biochemical data were retrospectively evaluated from 133 cold-stunned loggerhead turtles that were admitted for rehabilitation between 2008 and 2016. Convalescent data were compared with initial data for 24 turtles for which paired data were available. Convalescent values for white blood cell count, heterophil count creatine kinase, lactate dehydrogenase, glucose, and uric acid were significantly lower than initial values, whereas convalescent eosinophil count, alanine aminotransferase, aspartate aminotransferase, albumin, gamma-glutamyl transferase, total protein, globulin, blood urea nitrogen, calcium, phosphorus, chloride, and potassium were significantly higher. Results indicate that cold-stunned loggerhead turtles may be affected by dehydration, reduced renal function, cellular injury, deranged metabolic status, and activation of the adrenocortical stress response. Specific derangements associated with mortality could not be statistically characterized because only four turtles died.

Iohexol clearance testing was used to determine glomerular filtration rates (GFR) for 12 juvenile Kemp's ridley turtles (Lepidochelys kempii) that stranded because of cold-stunning. Iohexol was injected intravenously at 75 mg/kg, with subsequent plasma collection at 4, 8, and 24 h post-injection for measurement of iohexol iodine concentrations by inductively coupled plasma mass spectrometry (ICP-MS). Initial GFR was determined on median day 4 of hospitalization (range day 2–5) at an average body temperature of 19°C (66°F) (range 18–21°C [64–70°F]). Mean initial GFR was 4.6 mL/kg/h (range 1.9–8.7 mL/kg/h, n = 10). Convalescent GFR was determined on median day 126 of hospitalization (range day 108–232) at an average body temperature of 24°C (75°F) (range 23–25°C [74–77°F]). Mean convalescent GFR was 13.5 mL/kg/h (range 8.5–21.5 mL/kg/h, n = 10). Statistical analysis of paired initial and convalescent data demonstrated a significantly lower initial GFR, body weight, straight carapace length, and bod...

Juvenile Kemp’s ridley sea turtles were studied before and after ground transportation to assess potential transportation stress. Turtles appeared mildly stressed after a 13h transport (mild elevations in glucose) and moderately stressed by a 26h transport (more pronounced elevations in corticosterone and glucose), but remained in good clinical health., Sea turtle rehabilitation centres frequently transport sea turtles for long distances to move animals between centres or to release them at beaches, yet there is little information on the possible effects of transportation-related stress (‘transport stress’) on sea turtles. To assess whether transport stress is a clinically relevant concern for endangered Kemp’s ridley sea turtles (Lepidochelys kempii), we obtained pre-transport and post-transport plasma samples from 26 juvenile Kemp’s ridley sea turtles that were transported for 13 h (n = 15 turtles) or 26 h (n = 11 turtles) by truck for release at beaches. To control for effects of handling, food restriction and time of day, the same turtles were also studied on ‘control days’ 2 weeks prior to transport, i.e. with two samples taken to mimic pre-transport and post-transport timing, but without transportation. Blood samples were analysed for nine clinical health measures (pH, pCO2, pO2, HCO3, sodium, potassium, ionized calcium, lactate and haematocrit) and four ‘stress-associated’ parameters (corticosterone, glucose, white blood cell count and heterophil-to-lymphocyte ratio). Vital signs (heart rate, respiratory rate and cloacal temperature) were also monitored. Corticosterone and glucose showed pronounced elevations due specifically to transportation; for corticosterone, this elevation was significant only for the longer transport duration, whereas glucose increased significantly after both transport durations. However, clinical health measures and vital signs showed minimal or no changes in response to any sampling event (with or without transport), and all turtles appeared to be in good clinical health after both transport durations. Thus, transportation elicits a mild, but detectable, adrenal stress response that is more pronounced during longer durations of transport; nonetheless, Kemp’s ridley sea turtles can tolerate ground transportation of up to 26 h in good health. These results are likely to depend on specific transportation and handling protocols.