Deciphering coral disease dynamics: integrating host, microbiome, and the changing environment

Diseases of tropical reef organisms is an intensive area of study, but despite significant advances in methodology and the global knowledge base, identifying the proximate causes of disease outbreaks remains difficult. The dynamics of infectious wildlife diseases are known to be influenced by shifting interactions among the host, pathogen, and other members of the microbiome, and a collective body of work clearly demonstrates that this is also the case for the main foundation species on reefs, corals. Yet, among wildlife, outbreaks of coral diseases stand out as being driven largely by a changing environment. These outbreaks contributed not only to significant losses of coral species but also to whole ecosystem regime shifts. Here we suggest that to better decipher the disease dynamics of corals, we must integrate more holistic and modern paradigms that consider multiple and variable interactions among the three major players in epizootics: the host, its associated microbiome, and the environment. In this perspective, we discuss how expanding the pathogen component of the classic host-pathogen-environment disease triad to incorporate shifts in the microbiome leading to dysbiosis provides a better model for understanding coral disease dynamics. We outline and discuss issues arising when evaluating each component of this trio and make suggestions for bridging gaps between them. We further suggest that to best tackle these challenges, researchers must adjust standard paradigms, like the classic one pathogen-one disease model, that, to date, have been ineffectual at uncovering many of the emergent properties of coral reef disease dynamics. Lastly, we make recommendations for ways forward in the fields of marine disease ecology and the future of coral reef conservation and restoration given these observations

The dynamics of bacterial populations associated with corals and the possible role of bacterial pathogens in coral bleaching

The coral holobiont is known to comprise a diverse array of microbial partners, including the dinoflagellate endosymbiont, Symbiodinium, and bacteria living both on and within coral tissues, but little is known about the contributions that bacterial communities make to the overall partnership or how they interact with other microbial partners. Research described in this thesis aimed to understand coral- associated bacterial communities on the Great Barrier Reef and the nature of their interactions with Symbiodinium partners. Bacterial diversities documented on three common reef corals, Acropora millepora, A. tenuis and A. valida, confirmed that corals associate with specific microbiota. According to three culture-independent techniques [denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (t-RFLP) and clone libraries], consistent bacterial profiles were also conserved among all three species of Acropora within each of two study locations (Magnetic Is and Orpheus Is reefs), suggesting that closely related corals of the same genus harbor similar bacterial types. Bacterial community profiles of A. millepora at Orpheus Island were consistent throughout the year, indicating a stable community despite seasonal variation in environmental parameters. However, clone libraries, DGGE and t-RFLP profiles revealed bacterial communities grouped according to location rather than coral species. To further investigate the influence of environmental factors on coral- microbial associations, adult colonies of A. millepora were reciprocally translocated between two nearshore reefs (Magnetic Island and Great Keppel Island reefs) that differed in temperature. Clone libraries and DGGE profiles for corals placed on galvanized iron racks revealed that bacterial communities differed from those associated with in situ corals at Magnetic Island. Lack of change in bacterial communities of translocated corals through two bleaching events (a cold water bleaching on Great Keppel Island reef and a warm water bleaching at Magnetic Island reef) suggests that the rack environment of translocated corals was more important in shaping bacterial communities associated with Acropora millepora than the reef environment to which they were translocated. Nutrient inputs, such as metal derived Fe²⁺, may have influenced the bacteria present on translocated corals and should be considered in manipulative studies. A study comparing bacterial communities on 9-month old juvenile corals hosting either type C1 or D Symbiodinium suggested that coral-associated bacteria are not linked to Symbiodinium type in hospite, at least during early ontogeny. However, in contrast to bacterial profiles of adult corals, bacterial communities associated with juvenile corals were highly variable, indicating that bacterial associates are not conserved in these early stages. When 12-month old juveniles were sampled again in summer, bacterial communities associated with A. tenuis hosting clade D Symbiodinium were dominated by sequences affiliating with Vibrio species, indicating that corals harbouring this symbiont may be more susceptible to temperature stress, allowing growth of opportunistic microbial community members, possibly detrimental to coral health. To further investigate the role that temperature may play in the complex interactions of the coral holobiont, a controlled temperature experiment was undertaken with bacterial community shifts assessed in relation to coral Symbiodinium type. Shifts in bacterial associates on juvenile corals harboring ITS 1 type D Symbiodinium were observed when placed in a high (32°C) temperature treatment. In particular, there was a marked increase in the number of retrieved Vibrio-affiliated sequences, which coincided with a marked decline in their photochemical efficiency. In contrast, A. tenuis hosting ITS 1 type C1 Symbiodinium did not exhibit major bacterial shifts in the elevated temperature treatment, indicating a more stable bacterial community during thermal stress; concomitantly a decline in photochemical efficiency was minimal for this group. The lower resilience of A. tenuis to thermal stress when harbouring Symbiodinium D highlights the importance of inter-kingdom interactions among the coral host, dinoflagellate endosymbiont and bacterial associates for coral health and resilience. Comparisons of healthy vs. bleached coral metagenomic datasets revealed major shifts in microbial associates during heat stress, including shifts in Bacteria, Archaea, viruses, Fungi and micro-algae. The microbial community shifted from an autotrophic to a heterotrophically-driven metabolism, as evidenced by increases in fatty acid, protein, simple carbohydrate, phosphorus, and sulfur metabolism genes. The proportion of virulence genes was also higher in the bleached sample, indicating that bleaching may contribute to an increase in microorganisms capable of pathogenesis. These results demonstrate that thermal stress can result in shifts in coral-associated microbial communities, which may lead to deteriorating coral health

The function of mig-10 in axon guidance

The gene, mig-10, is necessary for the proper development of the various neurons in Caenorhabditis elegans. The mig-10 gene was characterized by observing the phenotypic effects a null mutation had on neuron development using transgenic strains and the fluorescent dy, DiO. Defects were observed in process and cell body position in the amphid sensory neurons. By staining with an antibody to a protein of known expression pattern, we found that mig-10 is likely expressed in neurons rather than hypodermal and glial cells

Metagenomic analysis of the coral holobiont during a natural bleaching event on the Great Barrier Reef

Understanding the effects of elevated seawater temperatures on each member of the coral holobiont (the complex comprised of coral polyps and associated symbiotic microorganisms, including Bacteria, viruses, Fungi, Archaea and endolithic algae) is becoming increasingly important as evidence accumulates that microbial members contribute to overall coral health, particularly during thermal stress. Here we use a metagenomic approach to identify metabolic and taxonomic shifts in microbial communities associated with the hard coral Acropora millepora throughout a natural thermal bleaching event at Magnetic Island (Great Barrier Reef). A direct comparison of metagenomic data sets from healthy versus bleached corals indicated major shifts in microbial associates during heat stress, including Bacteria, Archaea, viruses, Fungi and micro-algae. Overall, metabolism of the microbial community shifted from autotrophy to heterotrophy, including increases in genes associated with the metabolism of fatty acids, proteins, simple carbohydrates, phosphorus and sulfur. In addition, the proportion of virulence genes was higher in the bleached library, indicating an increase in microorganisms capable of pathogenesis following bleaching. These results demonstrate that thermal stress results in shifts in coral-associated microbial communities that may lead to deteriorating coral health

Bacterial communities of juvenile corals infected with different Symbiodinium (dinoflagellate) clades

The coral holobiont consists of the host and its microbial partners, including the dinoflagellate endosymbiont Symbiodinium and bacteria living both on and within coral tissues. Although genetically different, Symbiodinium types have been shown to differentially affect the physiology of\ud the coral host; their effects on the bacterial partners in the association are unknown. The present study compares profiles of the bacterial communities associated with juvenile corals of Acropora millepora and A. tenuis that had been experimentally infected with 2 different clades of Symbiodinium, Clade C1 and D, to investigate possible interactions between bacterial and Symbiodinium\ud communities. Three culture-independent 16S rRNA gene profiling methods (clone library construction,\ud terminal restriction length polymorphism and denaturing gradient gel electrophoresis) revealed no discernible pattern in bacterial communities on 9 mo old juvenile corals containing different clades of zooxanthellae, suggesting that coral-associated bacteria are not linked to Symbiodinium types in hospite in early ontogeny. In contrast to bacterial profiles of adult corals, bacterial communities associated with juvenile corals were highly variable, indicating that bacterial associates are not\ud conserved in these early stages. When 12 mo old juveniles were sampled again in summer, bacterial communities associated with A. tenuis hosting Clade D Symbiodinium were dominated by sequences affiliating with Vibrio species, indicating that corals harbouring this symbiont may be more susceptible to temperature stress, allowing growth of opportunistic microbial community members possibly\ud detrimental to coral health

Methods for sampling free-living Symbiodinium (zooxanthellae) and their distribution and abundance at Lizard Island (Great Barrier Reef)

The abundance and distribution of free-living dinoflagellates in the genus Symbiodinium have important implications for the ecology of coral reefs, determining both the symbionts available to newly recruited corals and symbiont types available for uptake by adult corals during environmental stress. However, little is known about where symbiotic dinoflagellates reside outside the host, due to the difficulty of capturing and detecting unicellular organisms in the marine environment. This study presents a successful protocol for sampling Symbiodinium from both the benthos and the water column. Comparisons of two detection methods for enumerating Symbiodinium indicated that conventional microscope analysis is accurate and more efficient when estimating Symbiodinium densities in sediment samples, while an automated particle counter (FlowCAM) was more efficient in detecting cells in the water column where densities are low. Symbiodinium densities were found to be relatively high (1000–4000 cells/mL) in sediment samples and much lower (up to 80 cells/mL) in the water column, indicating that the free-living form resides mainly in the benthos. Symbiodinium densities were found to be highly variable spatially, differing significantly between two reef locations. Within sites, elevated densities of Symbiodinium along reef margins combined with significant decreases in densities one meter away from the reef, suggest that cells aggregate within the reef habitat

Environmental management information system for Thailand's industrial estates.

Our project team designed an Environmental Management Information System prototype for the Industrial Estate Authority of Thailand. By providing effective data management, this tool is a first step toward sustainable development. Using our data analysis methods, and following our recommendations for implementation, the Industrial Estate Authority will be able to build a system that improves decision making throughout Thailand's Industrial Estates. The long-term benefits of this project include reduced waste, increased recycling, and overall environmental and economic improvement

Coastal urbanization influences human pathogens and microdebris contamination in seafood

Seafood is one of the leading imported products implicated in foodborne outbreaks worldwide. Coastal marine environments are being increasingly subjected to reduced water quality from urbanization and leading to contamination of important fishery species. Given the importance of seafood exchanged as a global protein source, it is imperative to maintain seafood safety worldwide. To illustrate the potential health risks associated with urbanization in a coastal environment, we use next-generation high-throughput amplicon sequencing of the 16S ribosomal RNA gene combined with infrared spectroscopy to characterize and quantify a vast range of potential human bacterial pathogens and microdebris contaminants in seawater, sediment and an important oyster fishery along the Mergui Archipelago in Myanmar. Through the quantification of >1.25 million high-quality bacterial operational taxonomic unit (OTU) reads, we detected 5459 potential human bacterial pathogens belonging to 87 species that are commonly associated with gut microbiota and an indication of terrestrial runoff of human and agricultural waste. Oyster tissues contained 51% of all sequenced bacterial pathogens that are considered to be both detrimental and of emerging concern to human health. Using infrared spectroscopy, we examined a total of 1225 individual microdebris particles, from which we detected 78 different types of contaminant materials. The predominant microdebris contaminants recovered from oyster tissues included polymers (48%), followed by non-native minerals (20%), oils (14%) and milk supplement powders (14%). Emerging technologies provide novel insights into the impacts of coastal development on food security and risks to human and environmental health