Aquarium Viromes: Viromes of Human-Managed Aquatic Systems

An aquarium ecosystem is home to many animal species providing conditions similar to native aquatic habitats but under highly controlled management. With a growing interest in understanding the interaction of microbiomes and resident animal health within aquarium environments, we undertook a metagenomic survey of viromes in seven aquarium systems with differing physicochemical and resident animal profiles. Our results show that a diverse array of viruses was represented in aquarium viromes, many of which were widespread in different aquarium systems (27 common viral families in all of the aquarium systems). Most viromes were dominated by DNA phages of the order Caudovirales as commonly found in other aquatic environments with average relative abundance greater than 64%. The composition and structure of aquarium viromes were associated with controlled system parameters, including nitrate, salinity, and temperature as well as resident animal profiles, indicating the close interaction of viromes with aquarium management practices. Furthermore, finding human associated viruses in a touch exhibit suggested that exposure of aquarium systems to human contact may lead to introduction of human cutaneous viruses into aquaria. This is consistent with the high abundance of skin microflora on the palms of healthy individuals and their detection in recreational waters, such as swimming pools. Lastly, assessment of antibiotic resistance genes (ARGs) in aquarium viromes revealed a unique signature of ARGs in different aquarium systems with trimethoprim being the most common. This is the first study to provide vital information on viromes and their unique relationships with management practices in a human-built and controlled aquarium environment

Aquarium microbiome response to ninety-percent system water change : clues to microbiome management

Author Posting. © John Wiley & Sons, 2015. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Zoo Biology 34 (2015): 360-367, doi:10.1002/zoo.21220.The bacterial community composition and structure of water from an established teleost fish system was examined before, during and after a major water change to explore the impact of such a water-change disturbance on the stability of the aquarium water microbiome. The diversity and evenness of the bacterial community significantly increased following the 90% water replacement. While the change in bacterial community structure was significant, it was slight, and was also weakly correlated with changes in physicochemical parameters. Interestingly there was a significant shift in the correlative network relationships between operational taxonomic units from before to after the water replacement. We suggest this shift in network structure is due to the turnover of many taxa during the course of water replacement. These observations will inform future studies into manipulation of the microbiome by changing system environmental parameter values to optimize resident animal health.Sean Gibbons was supported by an EPA STAR Graduate Fellowship.2016-05-2

Aquatic Mammals

Abstract Twenty neonatal harbor seal (Phoca vitulina) pups in rehabilitation following maternal separation underwent serial echocardiographic studies to assess patency and subsequent age of functional closure of the ductus arteriosus (d.a.). B-mode, color-flow Doppler, and pulse and continuous wave Doppler were utilized to identify the d.a. and determine patency and directionality of blood flow. Seals were also evaluated for evidence of foramen ovale (f.o.) patency. B-mode ultrasound was used to evaluate the inter-atrial septum for abnormal (aneurismal) motion, a sign of f.o. patency in other species. In one harbor seal, this motion was confirmed as being consistent with f.o. patency by contrast echocardiography. Closure of the f.o. was not confirmed in any harbor seal prior to release back into the free-ranging population. Data acquired indicate that there is patency of the f.o. and d.a. after birth for a longer period in phocids than in described terrestrial mammals

Deadly diving? Physiological and behavioural management of decompression stress in diving mammals

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the Royal Society B Biological Sciences 279 (2012): 1041-1050, doi:10.1098/rspb.2011.2088.Decompression sickness (DCS; ‘the bends’) is a disease associated with gas uptake at pressure. The basic pathology and cause are relatively well known to human divers. Breath-hold diving marine mammals were thought to be relatively immune to DCS owing to multiple anatomical, physiological and behavioural adaptations that reduce nitrogen gas (N2) loading during dives. However, recent observations have shown that gas bubbles may form and tissue injury may occur in marine mammals under certain circumstances. Gas kinetic models based on measured time-depth profiles further suggest the potential occurrence of high blood and tissue N2 tensions. We review evidence for gas-bubble incidence in marine mammal tissues and discuss the theory behind gas loading and bubble formation. We suggest that diving mammals vary their physiological responses according to multiple stressors, and that the perspective on marine mammal diving physiology should change from simply minimizing N2 loading to management of the N2 load. This suggests several avenues for further study, ranging from the effects of gas bubbles at molecular, cellular and organ function levels, to comparative studies relating the presence/absence of gas bubbles to diving behaviour. Technological advances in imaging and remote instrumentation are likely to advance this field in coming years.This paper and the workshop it stemmed from were funded by the Woods Hole Oceanographic Institution Marine Mammal Centre

Cancer Biomarker Discovery: The Entropic Hallmark

Background: It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. Methodology/Principal Findings: Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. Conclusions/Significance: We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-throughput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases

Whale-Associated Microbial Communities Remain Remarkably Stable despite Massive Water Community Disruption in a Managed Artificial Marine Environment

Highly managed and built environments such as zoos and aquaria provide a rich source of standardized environmental monitoring data over periods of years to decades. A fifty percent water change in an 11.4-million-liter indoor artificial sea water system housing three species of marine mammals was conducted over a two-month period. Using 16S rRNA gene sequencing, the microbial community structure of the system water and three host sites (feces, skin, and exhaled breath “chuff”) of whales housed in the system were characterized. Diversity measures confirmed massive disruption to the water community structure as an expected result of the water change. Host site-associated communities remained remarkably stable. Improved understanding of host microbial community dynamics in response to environmental system perturbations allows for sound management decisions toward optimizing conditions for resident animals

Inflation and deflation pressure-volume loops in anesthetized pinnipeds confirms compliant chest and lungs

We examined structural properties of the marine mammal respiratory system, and tested Scholander’s hypothesis that the chest is highly compliant by measuring the mechanical properties of the respiratory system in five species of pinniped under anesthesia (Pacific harbor seal, Phoca vitulina; northern elephant seal, Mirounga angustirostris; northern fur seal Callorhinus ursinus; California sea lion, Zalophus californianus; and Steller sea lion, Eumetopias jubatus). We found that the chest wall compliance (CCW) of all five species was greater than lung compliance (airways and alveoli, CL) as predicted by Scholander, which suggests that the chest provides little protection against alveolar collapse or lung squeeze. We also found that specific respiratory compliance was significantly greater in wild animals than in animals raised under human care. While differences in ages between the two groups may affect this incidental finding, it is also possible that lung conditioning in free-living animals may increase pulmonary compliance and reduce the risk of lung squeeze during diving. Overall, our data indicate that compliance of excised pinniped lungs provide a good estimate of total respiratory compliance

Gas bubble disease in the brain of a living California sea lion (Zalophus californianus)

A yearling California sea lion (Zalophus californianus) was admitted into rehabilitation with signs of cerebellar pathology. Diagnostic imaging that included radiography and magnetic resonance imaging (MRI) demonstrated space-occupying lesions predominantly in the cerebellum that were filled partially by CSF-like fluid and partially by gas, and cerebral lesions that were fluid filled. Over a maximum period of four months, the brain lesions reduced in size and the gas resorbed and was replaced by CSF-like fluid. To test the animal in this study for motor memory deficits, an alternation task in a two-choice maze was utilized. The sea lion performed poorly similar to another case of pneumocerebellum previously reported, and contrary to data acquired from a group of sea lions with specific hippocampal injury. The learning deficits were attributed to the cerebellar injury. These data provide important insight both to the clinical presentation and behavioral observations of cerebellar injury in sea lions, as well as providing an initial model for long-term outcome following cerebellar injury. The specific etiology of the gas could not be determined. The live status of the patient with recovery suggests that the most likely etiologies for the gas are either de novo formation or air emboli secondary to trauma. A small air gun pellet was present within and was removed from soft tissues adjacent to the tympanic bulla. While no evidence to support the pellet striking bone was found, altered dive pattern associated with this human interaction may have provided the opportunity for gas bubble formation to occur. The similarity in distribution of the gas bubble related lesions in this case compared with another previously published case of pneumocerebellum suggests that preferential perfusion of the brain, and more specifically the cerebellum, may occur during diving events