Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont.

Coral microbiomes are critical to holobiont health and functioning, but the stability of host-microbial interactions is fragile, easily shifting from eubiosis to dysbiosis. The heat-induced breakdown of the symbiosis between the host and its dinoflagellate algae (that is, "bleaching"), is one of the most devastating outcomes for reef ecosystems. Yet, bleaching tolerance has been observed in some coral species. This review provides an overview of the holobiont's diversity, explores coral thermal tolerance in relation to their associated microorganisms, discusses the hypothesis of adaptive dysbiosis as a mechanism of environmental adaptation, mentions potential solutions to mitigate bleaching, and suggests new research avenues. More specifically, we define coral bleaching as the succession of three holobiont stages, where the microbiota can (i) maintain essential functions for holobiont homeostasis during stress and/or (ii) act as a buffer to mitigate bleaching by favoring the recruitment of thermally tolerant Symbiodiniaceae species (adaptive dysbiosis), and where (iii) environmental stressors exceed the buffering capacity of both microbial and dinoflagellate partners leading to coral death.

Parentage analyses identify local dispersal events and sibling aggregations in a natural population of Millepora hydrocorals, a free-spawning marine invertebrate.

Dispersal is a critical process for the persistence and productivity of marine populations. For many reef species, there is increasing evidence that local demography and self-recruitment have major consequences on their genetic diversity and adaptation to environmental change. Yet empirical data of dispersal patterns in reef-building species remain scarce. Here, we document the first genetic estimates of self-recruitment and dispersal distances in a free-spawning marine invertebrate, the hydrocoral Millepora cf. platyphylla. Using twelve microsatellite markers, we gathered genotypic information from 3,160 georeferenced colonies collected over 27,000 m2 of a single reef in three adjacent habitats in Moorea, French Polynesia; the mid slope, upper slope, and back reef. Although the adult population was predominantly clonal (85% were clones), our parentage analysis revealed a moderate self-recruitment rate with a minimum of 8% of sexual propagules produced locally. Assigned offspring often settled at <10 m from their parents and dispersal events decrease with increasing geographic distance. There were no discrepancies between the dispersal distances of offspring assigned to parents belonging to clonal versus nonclonal genotypes. Interhabitat dispersal events via cross-reef transport were also detected for sexual and asexual propagules. Sibship analysis showed that full siblings recruit nearby on the reef (more than 40% settled at <30 m), resulting in sibling aggregations. Our findings highlight the importance of self-recruitment together with clonality in stabilizing population dynamics, which may ultimately enhance local sustainability and resilience to disturbance.

Microbiome of the Black-Lipped Pearl Oyster Pinctada margaritifera, a Multi-Tissue Description With Functional Profiling.

Elucidating the role of prokaryotic symbionts in mediating host physiology has emerged as an important area of research. Since oysters are the world's most heavily cultivated bivalve molluscs, numerous studies have applied molecular techniques to understand the taxonomic and functional diversity of their associated bacteria. Here, we expand on this research by assessing the composition and putative functional profiles of prokaryotic communities from different organs/compartments of the black-lipped pearl oyster Pinctada margaritifera, a commercially important shellfish valued for cultured pearl production in the Pacific region. Seven tissues, in addition to mucous secretions, were targeted from P. margaritifera individuals: the gill, gonad, byssus gland, haemolymph, mantle, adductor muscle, mucus, and gut. Richness of bacterial Operational Taxonomic Units (OTUs) and phylogenetic diversity differed between host tissues, with mucous layers displaying the highest richness and diversity. This multi-tissues approach permitted the identification of consistent microbial members, together constituting the core microbiome of P. margaritifera, including Alpha- and Gammaproteobacteria, Flavobacteriia, and Spirochaetes. We also found a high representation of Endozoicimonaceae symbionts, indicating that they may be of particular importance to oyster health, survival and homeostasis, as in many other coral reef animals. Our study demonstrates that the microbial communities and their associated predicted functional profiles are tissue specific. Inferred physiological functions were supported by current physiological data available for the associated bacterial taxa specific to each tissue. This work provides the first baseline of microbial community composition in P. margaritifera, providing a solid foundation for future research into this commercially important species and emphasises the important effects of tissue differentiation in structuring the oyster microbiome.

Historical changes (1905-present) in catch size and composition reflect altering fisheries practices on a small Caribbean island.

Effective assessments of the status of Caribbean fish communities require historical baselines to adequately understand how much fish communities have changed through time. To identify such changes and their causes, we compiled a historical overview using data collected at the beginning (1905-1908), middle (1958-1965) and end (1984-2016) of the 20th century, of the artisanal fishing practices and their effects on fish populations around Curaçao, a small island in the southern Caribbean. We documented historical trends in total catch, species composition, and catch sizes per fisher per month for different types of fisheries and related these to technological and environmental changes affecting the island's fisheries and fish communities. We found that since 1905, fishers targeted species increasingly farther from shore after species occurring closer to shore had become rare. This resulted in surprisingly similar catches in terms of weight, but not composition. Large predatory reef fishes living close to shore (e.g., large Epinephelid species) had virtually disappeared from catches around the mid-20th century, questioning the use of data from this period as baseline data for modern day fish assessments. Secondly, we compared fish landings to in-situ counts from 1969 to estimate the relative contributions of habitat destruction and overfishing to the changes in fish abundance around Curaçao. The decline in coral dominated reef communities corresponded to a concurrent decrease in the abundance and diversity of smaller reef fish species not targeted by fishers, suggesting habitat loss, in addition to fishing, caused the observed declines in reef fish abundance around Curaçao.

The spread of bovine tuberculosis in Canadian shared pastures: Data, model, and simulations.

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is a chronic disease typical of cattle. Nonetheless, it can affect many mammals including humans, making it one of the most widespread zoonotic diseases worldwide. In industrialized countries, the main pathways of introduction of bTB into a herd are animal trade and contact with infected wildlife. In addition, for slow-spreading diseases with a long latent period such as bTB, shared seasonal pastures might be a between-herd transmission pathway, indeed farmers might unknowingly send infected animals to the pasture, since clinical signs are rarely evident in early infection. In this study, we developed a dynamic stochastic model to represent the spread of bTB in pastures. This was tailored to Canadian cow-calf herds, as we calibrated the model with data sourced from a recent bTB outbreak in Western Canada. We built a model for a herd with seasonal management, characterized by its partition into a group staying in the main facility and the remaining group(s) moving to summer pastures. We used this model to estimate the time of the first introduction of bTB into the herd. Furthermore, we expanded the model to include herds categorized as high-risk contacts with the index herd, in order to estimate the potential for disease spread on shared pastures. Finally, we explored two control scenarios to be applied to high-risk farms after the outbreak detection. Our results showed that the first introduction likely happened 3 to 5 years prior to the detection of the index herd, and the probability of bTB spreading in pastures was low, but not negligible. Nevertheless, the surveillance system currently in place was effective to detect potential outbreaks.

On the occurrence of intracolonial genotypic variability in highly clonal populations of the hydrocoral Millepora platyphylla at Moorea (French Polynesia).

Intracolonial genotypic variability is described in many colonial organisms and arises from mosaicism (somatic mutation) and/or chimerism (allogenic fusion). Both processes provide an additional source of genotypic variation in natural populations and raise questions on the biological significance of colonies having more than one genotype. Using fifteen microsatellite markers, we screened for potential genetic heterogeneity within Millepora platyphylla colonies, a hydrocoral species known for its extensive morphological plasticity among reef habitats. We aimed to determine whether mosaicism and chimerism were related to specific reef habitats and/or colony morphologies. Our results show that intracolonial genotypic variability was common (31.4%) in M. platyphylla at Moorea, French Polynesia, with important variations in its frequency among habitats (0-60%), while no effect of morphology was observed. Mosaicism seemed responsible for most of the genetic heterogeneity (87.5%), while chimerism was rarer. Some mosaics were shared among fire coral clones indicating that mutations could be spread via colony fragmentation. Further, the genotypic variability among clones suggests that colonies produced asexually through fragmentation have the potential to accumulate their own mutations over time. Such mutation dynamics might have important implications for the adaptive potential of long-lived reef-builder populations that are predominantly sustained through asexual reproduction.

Fire coral clones demonstrate phenotypic plasticity among reef habitats.

Clonal populations are often characterized by reduced levels of genotypic diversity, which can translate into lower numbers of functional phenotypes, both of which impede adaptation. Study of partially clonal animals enables examination of the environmental settings under which clonal reproduction is favoured. Here, we gathered genotypic and phenotypic information from 3,651 georeferenced colonies of the fire coral Millepora platyphylla in five habitats with different hydrodynamic regimes in Moorea, French Polynesia. In the upper slope where waves break, most colonies grew as vertical sheets ("sheet tree") making them more vulnerable to fragmentation. Nearly all fire corals in the other habitats are encrusting or massive. The M. platyphylla population is highly clonal (80% of the colonies are clones), while characterized by the highest genotype diversity ever documented for terrestrial or marine populations (1,064 genotypes). The proportion of clones varies greatly among habitats (≥58%-97%) and clones (328 clonal lineages) are distributed perpendicularly from the reef crest, perfectly aligned with wave energy. There are six clonal lineages with clones dispersed in at least two adjacent habitats that strongly demonstrate phenotypic plasticity. Eighty per cent of the colonies in these lineages are "sheet tree" on the upper slope, while 80%-100% are encrusting or massive on the mid slope and back reef. This is a unique example of phenotypic plasticity among reef-building coral clones as corals typically have wave-tolerant growth forms in high-energy reef areas.

Genetic diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci.

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coral Millepora platyphylla, an important reef-builder of Indo-Pacific reefs. We tested the cross-species amplification of these loci in five other species of the genus Millepora and analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target species M. platyphylla, among which twelve were polymorphic with 2-13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five other Millepora species revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean species M. complanata due to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species of Millepora. Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323-0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoan Millepora species creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

Population structure of the hydrocoral Millepora platyphylla in habitats experiencing different flow regimes in Moorea, French Polynesia.

While the fire coral Millepora platyphylla is an important component of Indo-Pacific reefs, where it thrives in a wide range of environments, the ecological and biological processes driving its distribution and population structure are not well understood. Here, we quantified this species' population structure in five habitats with contrasting hydrodynamic regimes in Moorea, French Polynesia; two in the fore reef: mid and upper slopes, and three in the lagoon: back, fringing and patch reefs. A total of 3651 colonies of fire corals were mapped and measured over 45,000 m2 of surveyed reef. Due to the species' sensitivity to fragmentation in response to strong water movement, hydrodynamic conditions (e.g. waves, pass and lagoonal circulation) corresponded to marked differences in colony size distributions, morphology and recruitment dynamics among habitats. The size structure varied among reef habitats with higher proportions of larger colonies in calm nearshore reefs (fringing and patch reefs), while populations were dominated by smaller colonies in the exposed fore reefs. The highest densities of fire corals were recorded in fore reef habitats (0.12-0.20 n.m-2) where the proportion of recruits and juveniles was higher at mid slope populations (49.3%) than on the upper slope near where waves break (29.0%). In the latter habitat, most colonies grew as vertical sheets on encrusting bases making them more vulnerable to colony fragmentation, whereas fire corals were encrusting or massive in all other habitats. The lowest densities of M. platyphylla occurred in lagoonal habitats (0.02-0.04 n.m-2) characterized by a combination of low water movement and other physical and biological stressors. This study reports the first evidence of population structure of fire corals in two common reef environments and illustrates the importance of water flow in driving population dynamic processes of these reef-building species.

Epidemiological and Evolutionary Inference of the Transmission Network of the 2014 Highly Pathogenic Avian Influenza H5N2 Outbreak in British Columbia, Canada.

The first North American outbreak of highly pathogenic avian influenza (HPAI) involving a virus of Eurasian A/goose/Guangdong/1/1996 (H5N1) lineage began in the Fraser Valley of British Columbia, Canada in late November 2014. A total of 11 commercial and 1 non-commercial (backyard) operations were infected before the outbreak was terminated. Control measures included movement restrictions that were placed on a total of 404 individual premises, 150 of which were located within a 3 km radius of an infected premise(s) (IP). A complete epidemiological investigation revealed that the source of this HPAI H5N2 virus for 4 of the commercial IPs and the single non-commercial IP likely involved indirect contact with wild birds. Three IPs were associated with the movement of birds or service providers and localized/environmental spread was suspected as the source of infection for the remaining 4 IPs. Viral phylogenies, as determined by Bayesian Inference and Maximum Likelihood methods, were used to validate the epidemiologically inferred transmission network. The phylogenetic clustering of concatenated viral genomes and the median-joining phylogenetic network of the viruses supported, for the most part, the transmission network that was inferred by the epidemiologic analysis.

Unusual duplication of the insulin-like receptor in the crustacean Daphnia pulex.

BACKGROUND: The insulin signaling pathway (ISP) has a key role in major physiological events like carbohydrate metabolism and growth regulation. The ISP has been well described in vertebrates and in a few invertebrate model organisms but remains largely unexplored in non-model invertebrates. This study is the first detailed genomic study of this pathway in a crustacean species, Daphnia pulex. RESULTS: The Daphnia pulex draft genome sequence assembly was scanned for major components of the ISP with a special attention to the insulin-like receptor. Twenty three putative genes are reported. The pathway appears to be generally well conserved as genes found in other invertebrates are present. Major findings include a lower number of insulin-like peptides in Daphnia as compared to other invertebrates and the presence of multiple insulin-like receptors (InR), with four genes as opposed to a single one in other invertebrates. Genes encoding for the Dappu_InR are likely the result of three duplication events and bear some unusual features. Dappu_InR-4 has undergone extensive evolutionary divergence and lacks the conserved site of the catalytic domain of the receptor tyrosine kinase. Dappu_InR-1 has a large insert and lacks the transmembranal domain in the ß-subunit. This domain is also absent in Dappu_InR-3. Dappu_InR-2 is characterized by the absence of the cystein-rich region. Real-time q-PCR confirmed the expression of all four receptors. EST analyses of cDNA libraries revealed that the four receptors were differently expressed under various conditions. CONCLUSIONS: Duplications of the insulin receptor genes might represent an important evolutionary innovation in Daphnia as they are known to exhibit extensive phenotypic plasticity in body size and in the size of defensive structures in response to predation.

An analysis of the movement of dairy cattle through 2 large livestock markets in the province of Ontario, Canada.

Data pertaining to the movement of dairy cattle through 2 large livestock markets in the province of Ontario were collected for 1 week per month throughout 2004. Counts and postal codes of sellers and buyers of adult dairy cattle, veal calves, and dairy calves were obtained. Three assumptions were made to represent the level of mixing among animals that could take place at the markets. We estimated the number of livestock holdings that could be exposed to a highly contagious disease agent, should infected animals have been sold through the market in the same week. The estimates ranged from 8 to 20 holdings, when assuming no mixing at the market, to 51 to 171 holdings when assuming complete mixing. These markets are important hubs in the dairy cattle movement network in Ontario and pose the risk of infecting a large number of livestock holdings should animals infected with a highly contagious disease agent pass through them.

The North American Animal Disease Spread Model: a simulation model to assist decision making in evaluating animal disease incursions.

The North American Animal Disease Spread Model is a stochastic, spatial, state-transition simulation model for the spread of highly contagious diseases of animals. It was developed with broad international support to assist policy development and decision making involving disease incursions. User-established parameters define model behavior in terms of disease progression; disease spread by animal-to-animal contact, contact with contaminated personnel or equipment, and airborne dissemination; and the implementation of control measures such as destruction and vaccination. Resources available to implement disease control strategies, as well as the direct costs associated with these strategies, are taken into consideration. The model records a wide variety of measures of the extent of simulated outbreaks and other characteristics. The graphical interface and output visualization features also make it a useful tool for training and preparedness exercises. This model is now being used to evaluate outbreak scenarios and potential control strategies for several economically important exotic animal diseases in the United States, Canada, and elsewhere. NAADSM is freely available via the Internet at http://www.naadsm.org.

Evaluating alternative approaches to managing animal disease outbreaks--the role of modelling in policy formulation.

Modelling is a powerful tool for informing development of policies for the control of animal diseases. By permitting the study of 'what if' scenarios, this tool can be used to help identify and evaluate strategies to reduce the number of animals destroyed to eradicate diseases. To be useful, models need to be fit for purpose and appropriately verified and validated. For informing disease control policy, modelling will be most useful when used before an outbreak, particularly in the areas of retrospective analysis of previous outbreaks, contingency planning, resource planning, risk assessments and training. Recent experience suggests that predictive modelling during actual outbreaks needs to be viewed and used with caution. It is important to recognise that models are just one tool for providing scientific advice and should not be considered in isolation from experimental studies and collection and analysis of epidemiological data. Collaborative studies and international cooperation can help address validation issues and improve the utility of models for emergency disease management. One such initiative, involving the 'Quadrilateral countries' (Australia, Canada, New Zealand and the United States), Ireland and the United Kingdom is discussed.

Simple models to assist in communicating key principles of animal disease control.

Aggressive actions for disease eradication, including animal disposal, can have serious impacts on the livestock industry, environment and public confidence. Coordinated efforts are required for effective, efficient and acceptable disease control and eradication. The authors summarise concepts from previous publications into a group of simple examples, schematic diagrams and basic equations. These simplified models may be used to communicate principles of disease control to livestock owners and workers, and to regulatory officials and policy-makers. Such stakeholders may not have time to study more complex models. It is hoped that a broader appreciation of key principles will compel stakeholders to act routinely in a manner that improves the prevention and control of infectious animal diseases.

Retrospective investigation of chronic wasting disease of cervids at the Toronto Zoo, 1973-2003.

The occurrence of chronic wasting disease (CWD) at the Toronto Zoo was investigated retrospectively, based on an examination of management, animal health, and postmortem records, and immunohistochemical studies. Records of animal movements, clinical signs, and postmortem findings were examined for all cervids 1973-2003. All available samples of fixed, wax-embedded lymphoid or central nervous system tissue from cervids that died at the Toronto Zoo from 1973 to 2003, > 12 months of age, were tested, using prion protein immunostaining. Chronic wasting disease prion antigen was detected in 8 of 105 animals tested: 7 mule deer and 1 black-tailed deer. The most likely method of introduction was the importation of CWD-infected animals from a zoo in the United States. Animal-to-animal contact and environmental contamination were the most likely methods of spread of CWD at the zoo. No mule deer left the Toronto Zoo site, and the last animal with CWD died in 1981. Historic findings and ongoing testing of cervids indicate that the Toronto Zoo collection has very low risk of currently being infected with CWD.

Chronic wasting disease in Canada: Part 1.

The purpose of part 1 is to provide an overview of published literature (1980-2002) on chronic wasting disease (CWD) to inform Canadian readers about the disease and to explain Canadian regulatory approaches to the surveillance and control of CWD. Much of the scientific information is drawn from American publications obtained from internet searches in PubMed and Medline databases. The following keywords were used: chronic wasting disease, prion, diagnosis, transmissible spongiform encephalopathies, CWD and deer, CWD and elk, and CWD and environment. The article also presents information from Canadian publications and unpublished observations, Canadian Food Inspection Agency (CFIA) documents, and both government and nongovernment internet Web sites. The article highlights some different features of CWD in Canada, as compared with the situation in the United States, and mentions public health implications of the disease. It also describes the basis for development of Canada's surveillance and control program. Part 2 will detail the activities and results of the surveillance and control program during 2000 to 2002 and discuss factors that will influence the feasibility of eradicating CWD. Chronic wasting disease appears to have been introduced into Canada through the importation of infected farmed elk from the United States in the late 1980s and early 1990s, at a time when little was known about the disease. Since then, eradication efforts in Canada have led to the control of the spread of CWD in the farmed elk industry. Still, management of this disease, especially in free-ranging cervids, is a challenge.