I am interested in coral reef research especially coral reef genomics. I did a Masters project on coral disease in the Egyptian Red Sea. This project provided baseline information on coral disease, coral bleaching, and other health issues that affect coral reefs in this region. I came to JCU to join the coral genomics program at the ARC centre of Excellence for coral reef studies to do research in coral reef genomics towards a PhD degree. I am working with Prof David Miller, Prof Bette Willis both from JCU and Dr David Bourne, the Australian Institiute of Marine Science (AIMS). My current research is focused on using ecological genomics and applying next generation sequencing to investigate the poorly understood symbiosis between corals and the newly discovered microalga, Chromera velia. Supervisors: Dr David G Bourne (AIMS), Prof Bette L Willis (JCU), and Prof David J Miller (JCU) Phone: +61416240442 Address: James Cook University
1 James Cook Dr., Douglas 4811 Townsville Queensland Australia
The Red Sea is one of the most important repositories of marine biodiversity in the world.It is t... more The Red Sea is one of the most important repositories of marine biodiversity in the world.It is the world's northernmost tropical sea. Coral reefs are among the most biologically diverse and economically important ecosystems on the planet. They provide vital services to human societies and industries. Coral reef ecosystems in the Red Sea are legendary with more than 250 species of hard corals representing the highest diversity in the Indian Ocean. Coral diseases are challenging the resilience of coral reef communities. Unfortunately, very little is currently known about the distribution and prevalence of coral diseases in the Red Sea reefs. This book aims to provide baseline knowledge of coral disease/syndrome, predation and other signs of compromised health affecting hard corals in the northern Egyptian Red Sea, and to identify coral species that were the most susceptible to each specific coral disease. This project is part of the work of Egypt’s coral reefs research group: Dr Hany A Abd-elsalam, Dr Abdel-Hamid A M Ali and Mr Amin R Mohamed.
Reef-building corals live in a mutualistic relationship with photosynthetic algae (family Symbiod... more Reef-building corals live in a mutualistic relationship with photosynthetic algae (family Symbiodiniaceae) that usually provide most of the energy required by the coral host. This relationship is sensitive to temperature stress; as little as a 1°C increase often leads to collapse of the association. This sensitivity has led to interest in the potential of more stress tolerant algae to supplement or substitute for the normal Symbiodiniaceae mutualists. In this respect, the apicomplexan-like microalga Chromera is of particular interest due to its greater temperature tolerance. We generated a de novo transcriptome for a Chromera strain isolated from a GBR coral ("GBR Chromera") and compared to those of the reference strain of Chromera ("Sydney Chromera"), and to those of Symbiodiniaceae (Fugacium kawagutii, Cladocopium goreaui and Breviolum minutum), as well as the apicomplexan parasite, Plasmodium falciparum. In contrast to the high sequence divergence among representatives of different genera within the family Symbiodiniaceae, the two Chromera strains featured low sequence divergence at orthologous genes, implying that they are likely to be conspecifics. Although KEGG categories provide few criteria by which true coral mutualists might be identified, they do supply a molecular rationalization that explains the ecological dominance of Cladocopium spp. amongst Indo-Pacific reef corals. The presence of HSP20 genes may contribute to the high thermal tolerance of Chromera. This article is protected by copyright. All rights reserved.
Disease is defined as a disorder of structure or function in an organism, which produces specific... more Disease is defined as a disorder of structure or function in an organism, which produces specific signs or symptoms and is not simply a direct result of physical injury. In scleractinian corals, as in all other organisms, diseased individuals show morphologically distinct lesions, which manifest themselves in alterations of colour, shape, size, or texture. Coral diseases are routinely described by macroscopic signs, with notes on the extent of tissue loss, tissue colour, and exposure of coral skeleton aiding in the nomenclature and diagnosis. However, despite their reported significance in reefs around the world, the aetiologies of the majority of diseases are still unknown and coral epidemiology remains poorly understood. The majority of published literature suggests numerous microorganisms are capable of causing coral disease, including bacteria, viruses, fungi, and protozoa. That said, the initial trigger for disease is often recorded as being abiotic factors such as temperature, UV exposure, pollution (such as heavy metals, and agricultural chemicals) or predation scars, for example. Coral diseases have been shown to be prevalent on both well-managed (for example marine protected areas) and unmanaged reefs alike. Despite the serious negative implications associated with coral disease, not all geographic areas are as well documented as others. For example, diseases affecting corals throughout the Red Sea are one of the least well explored and documented. Here we sum up the current knowledge of the diseases described on the reefs in this area and give a brief background into what is currently known about the cause of such diseases.
Despite the ecological significance of the relationship between reef‐building corals and intracel... more Despite the ecological significance of the relationship between reef‐building corals and intracellular photosynthetic dinoflagellates of the genus Symbiodinium, very little is known about the molecular mechanisms involved in its establishment. Indeed, microarray‐based analyses point to the conclusion that host gene expression is largely or completely unresponsive during the establishment of symbiosis with a competent strain of Symbiodinium. In this study, the use of Illumina RNA‐Seq technology allowed detection of a transient period of differential expression involving a small number of genes (1073 transcripts; <3% of the transcriptome) 4 h after the exposure of Acropora digitifera planulae to a competent strain of Symbiodinium (a clade B strain). This phenomenon has not previously been detected as a consequence of both the lower sensitivity of the microarray approaches used and the sampling times used. The results indicate that complex changes occur, including transient suppress...
Since the discovery of Chromera velia, a novel microalga in 2008 during a study of Australian cor... more Since the discovery of Chromera velia, a novel microalga in 2008 during a study of Australian coral symbionts, great interest in this new algal species has developed. C. velia is an important organism being considered to sit phylogenetically between the photosynthetic dinoflagellate algae and the parasitic Apicomplexa. C. velia has been detected and isolated from different scleractinian corals in Australia including corals of the Great Barrier Reef. However little is known about the ecology and genetics of this microorganism. The study aims to use next generation sequencing technology (Illumina RNAseq) to generate a reference transcriptome assembly of C. velia isolated from Montipora digitata at the GBR. Differential gene expression in altered experimental treatments is investigating the diversity and dynamics of C. velia transcripts (mRNAs). Cultures were subjected to heat shock, heat stress, cold shock, cold stress, and darkness with control cultures grown under normal conditions, cultures grown under mixotrophic condition and cultures containing motile/immotile stages. Analysis of the transcriptome of C. velia will provide genomic insight into this novel chromerid alga through identifying genes involved in various physiological and metabolic processes as investigated under different experimental conditions.
Photosynthetic eukaryotes, such as microalgae and plants, foster fundamentally important relation... more Photosynthetic eukaryotes, such as microalgae and plants, foster fundamentally important relationships with their microbiome based on the reciprocal exchange of chemical currencies. Among these, the dicarboxylate metabolite azelaic acid (Aze) appears to play an important, but heterogeneous, role in modulating these microbiomes, as it is used as a carbon source for some heterotrophs but is toxic to others. However, the ability of Aze to promote or inhibit growth, as well as its uptake and assimilation mechanisms into bacterial cells are mostly unknown. Here, we use transcriptomics, transcriptional factor coexpression networks, uptake experiments, and metabolomics to unravel the uptake, catabolism and toxicity of Aze on two microalgal-associated bacteria,PhycobacterandAlteromonas, whose growth is promoted or inhibited by Aze, respectively. We identify the first putative Aze transporter in bacteria, a ‘C4-TRAP transporter’, and show that Aze is assimilated through fatty acid degradatio...
Since the discovery of Chromera velia as a novel coral-associated microalga, this organism has at... more Since the discovery of Chromera velia as a novel coral-associated microalga, this organism has attracted interest because of its unique evolutionary position between the photosynthetic dinoflagellates and the parasitic apicomplexans. The nature of the relationship between Chromera and its coral host is controversial. Is it a mutualism, from which both participants benefit, a parasitic relationship, or a chance association? To better understand the interaction, larvae of the common Indo-Pacific reef-building coral Acropora digitifera were experimentally infected with Chromera, and the impact on the host transcriptome was assessed at 4, 12, and 48 h post-infection using Illumina RNA-Seq technology. The transcriptomic response of the coral to Chromera was complex and implies that host immunity is strongly suppressed, and both phagosome maturation and the apoptotic machinery is modified. These responses differ markedly from those described for infection with a competent strain of the co...
The Red Sea is one of the most important repositories of marine biodiversity in the world.It is t... more The Red Sea is one of the most important repositories of marine biodiversity in the world.It is the world's northernmost tropical sea. Coral reefs are among the most biologically diverse and economically important ecosystems on the planet. They provide vital services to human societies and industries. Coral reef ecosystems in the Red Sea are legendary with more than 250 species of hard corals representing the highest diversity in the Indian Ocean. Coral diseases are challenging the resilience of coral reef communities. Unfortunately, very little is currently known about the distribution and prevalence of coral diseases in the Red Sea reefs. This book aims to provide baseline knowledge of coral disease/syndrome, predation and other signs of compromised health affecting hard corals in the northern Egyptian Red Sea, and to identify coral species that were the most susceptible to each specific coral disease. This project is part of the work of Egypt’s coral reefs research group: Dr Hany A Abd-elsalam, Dr Abdel-Hamid A M Ali and Mr Amin R Mohamed.
Reef-building corals live in a mutualistic relationship with photosynthetic algae (family Symbiod... more Reef-building corals live in a mutualistic relationship with photosynthetic algae (family Symbiodiniaceae) that usually provide most of the energy required by the coral host. This relationship is sensitive to temperature stress; as little as a 1°C increase often leads to collapse of the association. This sensitivity has led to interest in the potential of more stress tolerant algae to supplement or substitute for the normal Symbiodiniaceae mutualists. In this respect, the apicomplexan-like microalga Chromera is of particular interest due to its greater temperature tolerance. We generated a de novo transcriptome for a Chromera strain isolated from a GBR coral ("GBR Chromera") and compared to those of the reference strain of Chromera ("Sydney Chromera"), and to those of Symbiodiniaceae (Fugacium kawagutii, Cladocopium goreaui and Breviolum minutum), as well as the apicomplexan parasite, Plasmodium falciparum. In contrast to the high sequence divergence among representatives of different genera within the family Symbiodiniaceae, the two Chromera strains featured low sequence divergence at orthologous genes, implying that they are likely to be conspecifics. Although KEGG categories provide few criteria by which true coral mutualists might be identified, they do supply a molecular rationalization that explains the ecological dominance of Cladocopium spp. amongst Indo-Pacific reef corals. The presence of HSP20 genes may contribute to the high thermal tolerance of Chromera. This article is protected by copyright. All rights reserved.
Disease is defined as a disorder of structure or function in an organism, which produces specific... more Disease is defined as a disorder of structure or function in an organism, which produces specific signs or symptoms and is not simply a direct result of physical injury. In scleractinian corals, as in all other organisms, diseased individuals show morphologically distinct lesions, which manifest themselves in alterations of colour, shape, size, or texture. Coral diseases are routinely described by macroscopic signs, with notes on the extent of tissue loss, tissue colour, and exposure of coral skeleton aiding in the nomenclature and diagnosis. However, despite their reported significance in reefs around the world, the aetiologies of the majority of diseases are still unknown and coral epidemiology remains poorly understood. The majority of published literature suggests numerous microorganisms are capable of causing coral disease, including bacteria, viruses, fungi, and protozoa. That said, the initial trigger for disease is often recorded as being abiotic factors such as temperature, UV exposure, pollution (such as heavy metals, and agricultural chemicals) or predation scars, for example. Coral diseases have been shown to be prevalent on both well-managed (for example marine protected areas) and unmanaged reefs alike. Despite the serious negative implications associated with coral disease, not all geographic areas are as well documented as others. For example, diseases affecting corals throughout the Red Sea are one of the least well explored and documented. Here we sum up the current knowledge of the diseases described on the reefs in this area and give a brief background into what is currently known about the cause of such diseases.
Despite the ecological significance of the relationship between reef‐building corals and intracel... more Despite the ecological significance of the relationship between reef‐building corals and intracellular photosynthetic dinoflagellates of the genus Symbiodinium, very little is known about the molecular mechanisms involved in its establishment. Indeed, microarray‐based analyses point to the conclusion that host gene expression is largely or completely unresponsive during the establishment of symbiosis with a competent strain of Symbiodinium. In this study, the use of Illumina RNA‐Seq technology allowed detection of a transient period of differential expression involving a small number of genes (1073 transcripts; <3% of the transcriptome) 4 h after the exposure of Acropora digitifera planulae to a competent strain of Symbiodinium (a clade B strain). This phenomenon has not previously been detected as a consequence of both the lower sensitivity of the microarray approaches used and the sampling times used. The results indicate that complex changes occur, including transient suppress...
Since the discovery of Chromera velia, a novel microalga in 2008 during a study of Australian cor... more Since the discovery of Chromera velia, a novel microalga in 2008 during a study of Australian coral symbionts, great interest in this new algal species has developed. C. velia is an important organism being considered to sit phylogenetically between the photosynthetic dinoflagellate algae and the parasitic Apicomplexa. C. velia has been detected and isolated from different scleractinian corals in Australia including corals of the Great Barrier Reef. However little is known about the ecology and genetics of this microorganism. The study aims to use next generation sequencing technology (Illumina RNAseq) to generate a reference transcriptome assembly of C. velia isolated from Montipora digitata at the GBR. Differential gene expression in altered experimental treatments is investigating the diversity and dynamics of C. velia transcripts (mRNAs). Cultures were subjected to heat shock, heat stress, cold shock, cold stress, and darkness with control cultures grown under normal conditions, cultures grown under mixotrophic condition and cultures containing motile/immotile stages. Analysis of the transcriptome of C. velia will provide genomic insight into this novel chromerid alga through identifying genes involved in various physiological and metabolic processes as investigated under different experimental conditions.
Photosynthetic eukaryotes, such as microalgae and plants, foster fundamentally important relation... more Photosynthetic eukaryotes, such as microalgae and plants, foster fundamentally important relationships with their microbiome based on the reciprocal exchange of chemical currencies. Among these, the dicarboxylate metabolite azelaic acid (Aze) appears to play an important, but heterogeneous, role in modulating these microbiomes, as it is used as a carbon source for some heterotrophs but is toxic to others. However, the ability of Aze to promote or inhibit growth, as well as its uptake and assimilation mechanisms into bacterial cells are mostly unknown. Here, we use transcriptomics, transcriptional factor coexpression networks, uptake experiments, and metabolomics to unravel the uptake, catabolism and toxicity of Aze on two microalgal-associated bacteria,PhycobacterandAlteromonas, whose growth is promoted or inhibited by Aze, respectively. We identify the first putative Aze transporter in bacteria, a ‘C4-TRAP transporter’, and show that Aze is assimilated through fatty acid degradatio...
Since the discovery of Chromera velia as a novel coral-associated microalga, this organism has at... more Since the discovery of Chromera velia as a novel coral-associated microalga, this organism has attracted interest because of its unique evolutionary position between the photosynthetic dinoflagellates and the parasitic apicomplexans. The nature of the relationship between Chromera and its coral host is controversial. Is it a mutualism, from which both participants benefit, a parasitic relationship, or a chance association? To better understand the interaction, larvae of the common Indo-Pacific reef-building coral Acropora digitifera were experimentally infected with Chromera, and the impact on the host transcriptome was assessed at 4, 12, and 48 h post-infection using Illumina RNA-Seq technology. The transcriptomic response of the coral to Chromera was complex and implies that host immunity is strongly suppressed, and both phagosome maturation and the apoptotic machinery is modified. These responses differ markedly from those described for infection with a competent strain of the co...
The mutualistic relationship between reef-building corals and intracellular photosynthetic dinofl... more The mutualistic relationship between reef-building corals and intracellular photosynthetic dinoflagellates of the genus Symbiodinium provides the foundation of the coral reef ecosystem. Disruption of this relationship leads to coral bleaching which is occurring on a large scale and poses a real threat to the survival of coral reefs. In spite of the great ecological significance of this partnership to coral reefs, little is currently known about the molecular mechanisms involved in the establishment and maintenance of the symbiosis. A number of studies have investigated host gene expression during the establishment of coral-algal symbiosis, but these have failed to detect host symbiosis-related signals. To better understand the early events occurring during the establishment of symbiosis, infection experiments were conducted during spawning in Sesoko Island, Okinawa, Japan in June 2013 using Acropora digitifera larvae and a competent strain of symbionts, Symbiodinium sp. clade B. Next generation sequencing (Illumina RNAseq) was used for the first time to follow coral transcriptome-wide gene expression after exposure to competent Symbiodinium at 4-, 12-, 48- h post infection. These experiments allowed the detection of transient transcriptomic in the coral during the initial infection period.
This study aimed to provide baseline knowledge of coral diseases prevalence and coral health at n... more This study aimed to provide baseline knowledge of coral diseases prevalence and coral health at nine reef sites in the northern Egyptian Red Sea: I (El-Ain Al-Sukhna), II (Ras Za’farana), III (Hurghada), IV (Ras Ghozlani), V (Old Quay), VI (Yolanda reef), VII (Ras Umm Sid, Sharm El-Sheikh), VIII (WoodHouse reef, Sharm El-Sheikh), and IX (canyon reef, Dahab). Sites IV, V and VI are located in Ras Mohamed, marine protected area. Field surveys of coral diseases and signs of compromised health in the studied reefs revealed a mean prevalence of 1.03%. Macroscopic observations were diagnosed as: black band disease (0.44%), white syndrome (0.13%), pink line syndrome (0.04%), ulcerative white spots (0.02%), skeletal eroding band (0.001%), coral bleaching (2.2%), Drupella cornus snail predation (0.1%), fish predation (0.2%), pigmentation response (0.13%), sediment damage (0.08%), algae overgrowth (0.06%) and sponge overgrowth (0.04%). Prevalence of coral diseases and bleaching were higher in non-MPA sites than in MPA sites. The highest prevalence of coral diseases was recorded on the coral Favia stelligera, followed by Porites lutea, and Goniastrea edwardsi. Enhanced local anthropogenic stresses and increasing sea surface temperature due to global warming are the suggested potential factors responsible for the initiation and the persistence of some coral diseases in the studied reefs.
Coral reefs were considered as the product of a mutualistic relationship between the corals and a... more Coral reefs were considered as the product of a mutualistic relationship between the corals and algae of the genus Symbiodinium. However, recent research has demonstrated that corals lives in close associations with large, diverse and specific populationsof other microorganisms collectively referred to as the coral holobiont. Symbiodinium belongs to a group of protists called alveolates and recently it has been established that a number of other related alveolates are also intimately associated with corals including: the newly discovered algal species Chromera. Currently, there is a great deal of interest in Chromera because it is thought to be the missing link between the photosynthetic dinoflagellates and the non-photosynthetic apicomplexans. Interestingly, all the members of the Apicomplexa are, so far, identified as parasitic organisms. Although the literature implies that Chromerais a coral symbiont, this hypothesis has not been rigorously tested; its close relationship to apicomplexans suggests that it might be a facultative parasite. The research project aims to establish the nature of the relationship between Chromera and corals by investigating its impact on coral health/fitness using molecular-based approaches. Gene expression levels will be compared in A.digitiferalarvae exposed to Chromera with larvae exposed to a compatible Symbiodinium strain (as a positive control), using the Illumina RNA seq technology. Stress and immune challenges have distinct transcriptomic signatures, as does the normal Symbiodinium infection process. Hence analysis of the transcriptomic impact of Chromera infection should shed some light on the nature of the association of this organism with coral.
Since the discovery of Chromera velia, a novel microalga in 2008 during a study of Australian cor... more Since the discovery of Chromera velia, a novel microalga in 2008 during a study of Australian coral symbionts, great interest in this new algal species has developed. C. velia is an important organism being considered to sit phylogenetically between the photosynthetic dinoflagellate algae and the parasitic Apicomplexa. C. velia has been detected and isolated from different scleractinian corals in Australia including corals of the Great Barrier Reef. However little is known about the ecology and genetics of this microorganism. The study aims to use next generation sequencing technology (Illumina RNAseq) to generate a reference transcriptome assembly of C. velia isolated from Montipora digitata at the GBR. Differential gene expression in altered experimental treatments is investigating the diversity and dynamics of C. velia transcripts (mRNAs). Cultures were subjected to heat shock, heat stress, cold shock, cold stress, and darkness with control cultures grown under normal conditions, cultures grown under mixotrophic condition and cultures containing motile/immotile stages. Analysis of the transcriptome of C. velia will provide genomic insight into this novel chromerid alga through identifying genes involved in various physiological and metabolic processes as investigated under different experimental conditions.
AsianScientist (Jun. 28, 2016) - Scientists in Japan and Australia have found that corals undergo... more AsianScientist (Jun. 28, 2016) - Scientists in Japan and Australia have found that corals undergo changes in gene expression within hours of when algae are introduced. Their results, published in Molecular Ecology, could help scientists better understand the symbiotic relationship between corals and algae.
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between corals and algae.