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Gut bacterial communities play a vital role in a host's digestion and fermentation of complex carbohydrates, absorption of nutrients, and energy harvest/storage. Dugongs are obligate seagrass grazers with an expanded hindgut and associated microbiome. Here, we characterised and compared the faecal bacterial communities of dugongs from genetically distinct populations along the east coast of Australia, between subtropical Moreton Bay and tropical Cleveland Bay. Amplicon sequencing of fresh dugong faecal samples (n=47) revealed Firmicutes (62%) dominating the faecal bacterial communities across all populations. Several bacterial genera (Bacteroides, Clostridium sensu stricto 1, Blautia and Polaribacter) were detected in samples from all locations, suggesting their importance in seagrass digestion. Principal coordinate analysis showed the three southern-most dugong populations having different faecal bacterial community compositions from northern populations. The relative abundances of the genera Clostridium sensu stricto 13 and dgA-11 gut group were higher, but Bacteroides was lower, in the southern dugong populations, compared to the northern populations, suggesting potential adaptive changes associated with location. This study contributes to our knowledge of the faecal bacterial communities of dugongs inhabiting Australian coastal waters. Future studies of diet selection in relation to seagrass availability throughout the dugong's range will help to advance our understanding of the roles that seagrass species may play in affecting the dugong's faecal bacterial community composition., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)

The dugong (Dugong dugon) is a marine mammal widely distributed throughout the Indo-Pacific and the Red Sea, with a Vulnerable conservation status, and little is known about many of the more peripheral populations, some of which are thought to be close to extinction. We present a de novo high-quality genome assembly for the dugong from an individual belonging to the well-monitored Moreton Bay population in Queensland, Australia. Our assembly uses long-read PacBio HiFi sequencing and Omni-C data following the Vertebrate Genome Project pipeline to reach chromosome-level contiguity (24 chromosome-level scaffolds; 3.16 Gbp) and high completeness (97.9% complete BUSCOs). We observed relatively high genome-wide heterozygosity, which likely reflects historical population abundance before the last interglacial period, approximately 125,000 yr ago. Demographic inference suggests that dugong populations began declining as sea levels fell after the last interglacial period, likely a result of population fragmentation and habitat loss due to the exposure of seagrass meadows. We find no evidence for ongoing recent inbreeding in this individual. However, runs of homozygosity indicate some past inbreeding. Our draft genome assembly will enable range-wide assessments of genetic diversity and adaptation, facilitate effective management of dugong populations, and allow comparative genomics analyses including with other sirenians, the oldest marine mammal lineage., (© The American Genetic Association. 2024.)

Non-invasively collected faecal samples are an alternative source of DNA to tissue samples, that may be used in genetic studies of wildlife when direct sampling of animals is difficult. Although several faecal DNA extraction methods exist, their efficacy varies between species. Previous attempts to amplify mitochondrial DNA (mtDNA) markers from faeces of wild dugongs (Dugong dugon) have met with limited success and nuclear markers (microsatellites) have been unsuccessful. This study aimed to establish a tool for sampling both mtDNA and nuclear DNA (nDNA) from dugong faeces by modifying approaches used in studies of other large herbivores. First, a streamlined, cost-effective DNA extraction method that enabled the amplification of both mitochondrial and nuclear markers from large quantities of dugong faeces was developed. Faecal DNA extracted using a new 'High Volume- Cetyltrimethyl Ammonium Bromide- Phenol-Chloroform-Isoamyl Alcohol' (HV-CTAB-PCI) method was found to achieve comparable amplification results to extraction of DNA from dugong skin. As most prevailing practices advocate sampling from the outer surface of a stool to maximise capture of sloughed intestinal cells, this study compared amplification success of mtDNA between the outer and inner layers of faeces, but no difference in amplification was found. Assessment of the impacts of faecal age or degradation on extraction, however, demonstrated that fresher faeces with shorter duration of environmental (seawater) exposure amplified both markers better than eroded scats. Using the HV-CTAB-PCI method, nuclear markers were successfully amplified for the first time from dugong faeces. The successful amplification of single nucleotide polymorphism (SNP) markers represents a proof-of-concept showing that DNA from dugong faeces can potentially be utilised in population genetic studies. This novel DNA extraction protocol offers a new tool that will facilitate genetic studies of dugongs and other large and cryptic marine herbivores in remote locations., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: Dr. Margaret E. Hunter who is an author on this paper currently serves on the editorial board of the PLOS ONE journal. This does not alter our adherence to PLOS ONE policies on sharing data and materials., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

Dugongs (Dugong dugon) are fully marine mammals that live independently of fresh water so must balance water and electrolytes in a hyperosmotic environment. To investigate osmoregulation, matched plasma and urine from 51 live wild dugongs were analysed for osmolality, major electrolytes (Na + , Cl - , K + ), urea, creatinine, and glucose. Maximum urine osmolality (1468 mOsm kg -1 ) and Na + , K + , and Cl - concentrations (757, 131.3, 677 mmol L -1 , respectively) indicate that dugongs are capable of concentrating urine above seawater and could potentially realise a net gain of free water from drinking seawater. However, mean urine osmolality of 925.4 (± 46.6) mOsm kg -1 suggests that mariposia is unlikely to be an important osmoregulatory mechanism. Dugongs may obtain enough preformed water from their seagrass diet and metabolic oxidation to maintain homeostasis. Mean plasma osmolality of 339.6 (± 1.8) mOsm kg -1 is higher than in the related manatees but within the range for fully marine cetaceans. Relatively high mean plasma Na + (175.5 ± 1.7 mmol L -1 ) and K + (6.9 ± 0.1 mmol L -1 ), as well as mean urinary Na + (469.6 ± 22.5 mmol L -1 ) and K + levels (32.5 ± 4.5 mmol L -1 ) may reflect a salt-rich seagrass diet. Pregnant females had higher mean plasma osmolality (355.3 ± 4.9 mmol L -1 ) than non-pregnant females and males (337.9 ± 1.7 mOsm kg -1 ), suggesting that fluid retention was not a feature of pregnancy. Further research on water intake and endocrinology will enhance our understanding of osmoregulation in dugongs.

Species-specific antibodies (Ab) for the measurement of immunoglobulins (Ig) are valuable tools for determining the humoral immune status of threatened and endangered wildlife species such as dugongs. However, no studies have reported antibody reagents against dugong immunoglobulin. The object of this study was to develop an Ab with specificity for dugong IgG and apply this tool to survey total IgG levels in plasma samples from a live wild population of dugongs in southern Queensland, Australia. Dugong IgG was isolated from plasma by protein A/G column chromatography and a polyclonal antiserum was successfully raised against the dugong IgG through immunization of mice. The anti-dugong antiserum was reactive with dugong serum but not immunoglobulin from other species such as rats and humans. When tested against a panel of dugong plasma samples, relative IgG levels from dugongs (n = 116) showed biologically relevant relationships with pregnancy status and a principal component of Body Mass Index (BMI)/globulin/fecal glucocorticosteroid (chronic stress) levels combined, which together accounted for 9.2% of the variation in total Ig levels. Together these data suggest that dugongs show variation in total IgG and that this correlates with some physiological parameters of dugong health., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Background: Little is known of the hematology of the dugong (Dugong dugon), a secretive and endangered coastal marine mammal., Objectives: This paper reports hematologic reference intervals (RI) for dugongs and characterizes morphologic, cytochemical, and ultrastructural features of dugong leukocytes., Methods: Blood was collected from live, apparently healthy dugongs and analyzed using Cell-Dyn 3700 or Sysmex XT-2000iV hematology analyzers. Blood films were subjected to a series of cytochemical stains, and leukocyte structure was examined using transmission electron microscopy., Results: Reference intervals were established for 14 hematologic variables, total solids, and fibrinogen for 92 dugongs. Significant differences in some variables were found for animal size class, sex, and pregnancy status, and between analyzers. Subadults had higher leukocyte and lymphocyte counts than adults. Males had higher total solids and fibrinogen than females. Pregnant females had higher HCT, MCV, and circulating nucleated RBC, and lower platelet counts than nonpregnant females. Lymphocytes were usually the predominant circulating leukocyte. Heterophil cytoplasmic granules were abundant, fine, round to ovoid, and intensely eosinophilic, and round to ovoid or rod-shaped, and variably electron dense in electron microscopy. Eosinophils contained larger round eosinophilic to orange cytoplasmic granules, which ultrastructurally were bicompartmental with a round eccentric electron-dense core. Cytochemical staining of dugong heterophils suggests biochemical similarity to those of manatees and elephants, and for eosinophils, similarity to those of elephants, ruminants, and equids., Conclusions: Generation of hematologic RI and characterization of leukocyte morphology improves evaluation of dugong health across this population and serves as a reference for other populations outside southern Queensland., (© 2015 American Society for Veterinary Clinical Pathology.)

Background: Little is known about the baseline clinical pathology of the dugong (Dugong dugon), a vulnerable marine mammal found in tropical coastal marine systems., Objectives: The purpose of the study was to collect and determine reference intervals (RI) for select serum biochemical variables for dugongs, and to analyze differences between males and females and different age groups., Methods: Reference intervals were established from 103 apparently healthy, wild-caught dugongs for 31 analytes using a Beckman Coulter AU400 Automated Chemistry Analyzer and an Olympus AU680 Chemistry-Immuno Analyzer., Results: Significant differences (P < .05) in some of the variables were found related to size class, sex, and pregnancy status. Adult dugongs had higher serum sodium, potassium, bicarbonate, glucose, and l-lactate concentrations and higher anion gap, compared to sub-adults. Male dugongs had higher triglyceride and l-lactate concentrations than females. Pregnant females displayed higher l-lactate levels compared to nonpregnant animals. Statistical differences in variables within the population contributed to better understanding of the physiologic differences between cohorts. Some serum biochemistry changes observed in this study here also potentially include some effects of pursuit on dugongs (eg, higher l-lactate); however, as all dugongs were subject to similar capture and handling, serum biochemistry RI should be considered as normal for captured dugongs., Conclusions: The serum biochemical RI documented here are considered representative of a population of healthy captured dugongs. They provide a baseline for health surveillance of this and other dugong populations., (© 2015 American Society for Veterinary Clinical Pathology.)

The dugong Dugong dugon is classified as Vulnerable to extinction but may be endangered in some regions. Cause of death in stranded dugongs has not been determined in a large proportion of animals examined, with investigations hindered by limited information on dugong health and diseases, and paucity of knowledge of common or endemic pathological findings. Here we describe pathological findings in harvested dugongs from the relatively pristine area of central Torres Strait, and we characterise lesions attributable to drowning. Other recorded lesions were mild and predominated by host reaction to the presence of trematodes within the gastrointestinal tracts, liver and pancreas. Ascarid worm burdens were low in comparison to dugongs from developed coastlines. Hepatocellular lipofuscin and ferritin pigmentation were commonly observed, more pronounced in livers of older animals and concurrent with periportal and bridging fibrosis. Lesions attributable to drowning included incomplete collapse of lungs, dorsal or diffuse pulmonary congestion, mild intra-alveolar haemorrhage and oedema, mild interstitial oedema and rupture of peripheral alveolar septae with acute myofibre fragmentation and degeneration. No accumulation of foam or aspiration of water or particulate matter was observed, suggesting that dugongs 'dry drown'. Morphometric features of normal spleen are also presented. Characterisation of common pathological findings and those attributable to drowning in this species will aid in the interpretation of post mortem findings for the significant number of dugongs found deceased along urbanised coastlines.

Determining the reproductive status of long-term captive animals is essential because the onset of sexual maturity and reproductive activity may necessitate changes in husbandry requirements. This study reports on the first multi-year reproductive hormone monitoring program for captive dugongs of both sexes using feces. Fecal samples were collected from one male (Pig) over 9 years (4-13.2y of age; n=288 samples, 0.8±0.1 samples per week from July 2007 to February 2012) and one female (Wuru) over 7 years (from neonate to 6.9 y; n=171 samples, 0.5±0.1 samples per week from July 2007 to February 2012), and from one solitary female dugong (Gracie) over 10 months (10.5-11.3y of age; n=54 samples, 1.1±0.2 sample per week from September 2008 to June 2009). Using enzyme-immunoassay, fecal progesterone (fP) and estradiol-17β (fE) concentrations were assayed in the two captive females, and testosterone (fT) concentration in the captive male, and compared these to concentrations in wild dugongs. Female Wuru exhibited increasing fP concentrations at 5+ y, indicating early onset of ovarian cycling typical of non-pregnant adult females. Female Gracie maintained basal fP concentrations consistent with wild immature dugongs, indicating that she had not reached puberty by 11y. Nutritional plane may account for differences in age at sexual maturity in these female dugongs. At age 3-4y, Wuru had fE concentrations 1.4 times greater than maximum concentrations recorded in all wild females, and these concentrations were coincident with a period of rapid weight gain. For the male Pig, increasing fT concentrations at 9y provided early indications of puberty. Pig's tusks erupted by 11y, and sexual maturity (indicated by spermatic semen) was confirmed by 12.8y. Identification of sexual maturation prompted two trials of a male contraceptive treatment using the GnRH agonist, deslorelin (9.4mg administered in 2010 and 15.6mg in 2011). Testosterone production was not significantly suppressed by these dosages, and treatment did not terminate sperm production at week 10-11 post-implantation, even at the larger dose tested. Routine analysis of fecal hormones was helpful for making reproductive management decisions regarding individual captives and in guiding the long-term captive management of this cryptic species., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Assessing reproductive status and monitoring reproductive rates is important in the effective management of vulnerable marine mammal species such as the dugong (Dugong dugon). Knowledge of the reproductive physiology of this species is limited, and determining reproductive parameters (e.g., sexual maturation, pregnancy, and reproductive senescence) has been restricted by a lack of non-lethal methods for assessing reproductive status in free-ranging individuals. The aim of this study was to develop a method to identify pregnant individuals in a wild dugong population. Using an enzymeimmunoassay, we quantified concentrations of fecal progesterone metabolites (fP) in 322 dugongs, including confirmed pregnant females (n=10), presumed non-pregnant adult females (n=25), juvenile females (n=24), subadult females (n=41), adult females of unknown pregnancy state (n=63), and males of all sizes (n=159). External body morphometrics of each dugong were measured, and confirmation of pregnancy in adult female dugongs was determined by ultrasonography or observation of subsequent neonates. Concentrations of fP were different between sexes and reproductive size classes (P<0.001), and ∼30-fold higher in confirmed pregnant dugongs (2017-7760 ng/g) compared to presumed non-pregnant females (30-221 ng/g), juvenile females (29-195 ng/g), and males (24-261 ng/g) (P<0.001). Body measures of maximum and anal girths, and teat length were all greater in confirmed pregnant females than presumed non-pregnant females (all P<0.05). We evaluated a Discriminant Function Analysis (DFA) to provide a model for predicting pregnant and non-pregnant dugongs. Cross-validated results showed that the DFA correctly classified 100% of pregnant and non-pregnant females using fP concentrations, body length, fineness ratio (an index of body shape), and teat length (a female reproductive trait). Using the DFA model, we classified the pregnancy status of all female dugongs and identified a total of 30 females as pregnant and 133 females as non-pregnant from the sampled population over the sample period. Pregnant dugongs in the Moreton Bay population are characterized by fecal progesterone metabolite concentrations > 1000 ng/g, body length ≥ 260 cm, maximum girth ≥ 215 cm, anal girth ≥ 126 cm, and teat length ≥ 5 cm long. In summary, analysis of fP concentrations in combination with body morphometrics may be used to diagnose pregnancy in free-ranging dugongs, and provides a new tool to monitor breeding rates of wild sirenian populations., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Knowledge of male reproductive status and activity in free-ranging animals is vital to understanding reproductive patterns and population dynamics. Until now, almost all information regarding reproductive behavior of the dugong, a cryptic marine mammal, has relied on post-mortem examination. We examined the relationships between body length, tusk eruption (secondary sexual characteristic), seasonality, and group association on fecal testosterone metabolite concentrations in 322 free-ranging dugongs (159 males, 163 females) in subtropical Moreton Bay, Australia. Fecal testosterone concentrations demonstrated biologically meaningful differences in testicular activity between sexes and across reproductive/age classes, and were correlated with circulating concentrations in serum. Male dugongs have a pre-reproductive period that persists until a body length of 240 cm is achieved. Puberty apparently occurs between 240 and 260 cm body length when fecal testosterone levels increase fourfold (>500 ng/g) over juvenile levels, and is associated with tusk eruption. However, social maturity may be delayed until male dugongs are larger than 260 cm with well-developed tusks. In mature males, the lowest (<500 ng/g) fecal testosterone concentrations occur in the austral autumn months with maximal concentrations in September-October, coincident with the onset of a spring mating season. During spring, solitary mature males had fecal testosterone concentrations double those of mature males sampled within groups, potentially suggesting a mating strategy involving roving of reproductively active males. This study demonstrates that single-point physiological data from individuals across a population have value as indicators of reproductive processes. Our approach provides an efficacious non-lethal method for the census of reproductive status and seasonality in live male dugongs.

Seven hundred fifty-one dugongs (Dugong dugon) were pursued, captured, and handled for up to 20 min for population sampling. Fifty of these dugongs were then removed from the water for up to 55 min for comprehensive medical examination. Fifty whole blood and separated serum samples were analyzed for potassium, sodium, chloride, creatinine kinase (CK), aspartate aminotransferase (AST), alanine aminotransferase (ALT), lactate dehydrogenase (LDH), urea, creatinine, glucose, anion gap, and total blood CO2. Serum biochemical variables of the dugong were compared with those obtained in previous studies of the related West Indian manatee, a mammal that does not appear to experience capture myopathy based on available data. Differences between these species included higher blood sodium and chloride in dugongs, which may reflect differences in salt balance and renal function, and higher blood lactate and CO2. Some biochemical analytes such as CK and AST, which may be indicative of rhabdomyolysis associated with capture stress myopathy (a potentially fatal condition for which dugongs have been thought to be highly susceptible) were high compared with levels previously measured in wild West Indian manatees (Trichechus latirostris). One of the 50 dugongs had marked elevations of CK and AST but showed no other clinical indications of rhabdomyolysis associated with capture myopathy such as hyperthermia. Rather, generally high levels of lactate, CK, and AST most probably reflect metabolic acidosis resulting from the exertion involved in the pursuit prior to capture. Earlier observations suggesting that dugongs were probably susceptible to capture stress myopathy (based on high serum potassium levels) were not supported by this study. Capture and handling methods currently used on dugongs in this research program do not appear to result in acute capture stress.