"If there is magic on this planet, it is contained in water."
-- Loren Eiseley

    The long-term objectives of our research program are to (a) discover and characterize novel ultrastructural systems associated with locomotion, feeding, symbioses, parasitism and photoreception; (b) gain deeper insights into the origins and functions of complex ultrastructural systems using single cell transcriptomics/genomics; (c) address specific hypotheses about ultrastructural character evolution using molecular phylogenetic methods; (d) accelerate the discovery and characterization of new and poorly known lineages of (uncultured) single-celled eukaryotes from diverse marine environments; and (e) understand major trends and reoccurring innovations in eukaryotic cell evolution. More focused research projects are motivated by these research themes.

Click here to read a lay report of our research program in UBC's Frontier Journal, Issue 3: (PDF).

    Research on the diversity of these eukaryotic cells is exploratory and progresses in four principal phases: (1) collection, isolation and cultivation of the organisms from nature (e.g. fieldwork at the Bamfield Marine Sciences Centre - click on image below), (2) identification, specimen preparation and description of the organisms using high resolution microscopy, (3) molecular characterization of the organisms and (4) computational analyses associated with digital image processing and comparative molecular biology. Outcomes of this research will accelerate the discovery and characterization of new and poorly known species of single-cellular eukaryotes from diverse environments (e.g., marine sediment interfaces and the water column) and identify novel ways in which unicellular predators have solved basic biological problems (cell locomotion, nutrition, and photoreception).

    Microbial eukaryotes in low oxygen environments are often enveloped with bacteria, but the diversity and functional significance of these relationships are poorly understood. The lab is continuing to characterize a distinct subgroup of euglenozoans, namely the Symbiontida (e.g., Calkinsia and Bihospites; left-side LM images below), from oxygen-depleted and sulfidic marine environments. By definition, all members of this group carry epibionts that are intimately associated with underlying mitochondrion-derived organelles beneath the surface of the hosts (i.e., putative hydrogenosomes). We have shown that some of these lineages have additional ultrastructural traits that facilitate these epibiotic interactions, such as a complex and stable extracellular matrix consisting of conduits between the host cell and the enveloping epibionts. Our ultrastructural and molecular evidence so far have demonstrated that at least two different lineages of epibiotic bacteria are associated with symbiontids: (1) rod-shaped sulfur or sulfide-oxidizing members of the epsilon proteobacteria and (2) spherical verrucomicrobia containing a tightly wound thread around a dense DNA core that is capable of rapid discharge (SEM and TEMs shown below). Epsilon proteobacteria have a significant role in deep-sea habitats as primary colonizers, primary producers and/or in symbiotic associations, so these epibionts might detoxify the immediate environment for the eukaryotic hosts. The spherical verrucomicrobia, by contrast, are capable of rapid evisceration of the chromosome and thread through an apical pore, which potentially extends their lifecycle through extrusive sporulation. The features of these bacteria are enigmatic but provide context for inferring lateral symbiont transfer, convergent evolution, and potentially the origins of extrusomes across the tree of eukaryotes. The eukaryotic hosts likely serve as a motile substrate that delivers the epibionts to ideal locations with respect to the oxic/anoxic interface, perhaps allowing the host to cultivate a food source. We are interested in gaining much deeper insights into the overall diversity and basic biology of these particular hosts and epibionts. Because symbiontid isolates and environmental DNA sequences from this clade have now been recovered from many locations worldwide, symbiontids are expected to be much more widespread and diverse than presently appreciated. Projects in the lab will continue to address this diversity using a combination of comparative ultrastructural and molecular approaches, including single cell genomics/transcriptomics.

    Our research explores the diversity and evolutionary history of cellular traits in marine meiofaunal organisms, including several very distantly related lineages of single-celled eukaryotes (e.g., euglenozoans, dinoflagellates and cryomonad cercozoans) and miniaturized animals (e.g., scalidophorans and turbellarians). The lab is interested in the broad patterns and processes of convergent evolution associated with this lifestyle and how lineages of “microbial” animals, single-celled eukaryotes and bacteria living in the same environments interact with each other. Some current research projects in the lab are focused on the biology and overall diversity of turbellarians and scalidophorans (i.e., kinorhynchs, loriciferans and priapulids) using confocal microscopy, FIB-SEM, transcriptomics and DNA barcoding. Many meiofaunal animals have co-evolved with symbionts and have acquired extremely reduced anatomical/physiological traits associated with miniaturization.

    Other projects are focused on characterizing the cellular traits of euglenids (left-most image shown below), dinoflagellates (second and third images from the left, shown below) and cryomonad cercozoans (two right-hand images shown below), which are diverse and poorly understood groups of microbial eukaryotes that inhabit marine sediments. Although all three groups have adopted similar modes of predatory life and thrive as part of the same microbial communities within marine sand, they could not be more distantly related to one another: euglenids are part of a supergroup called the Excavata; dinoflagellates are part of a supergroup called the Alveolata; and cryomonads are part of a supergroup called the Rhizaria. Despite these vast phylogenetic distances, some members within each of these groups look remarkably similar to one another at many different levels. For instance, all three of these groups have independently acquired a large and diverse suite of ultrastructural features, such as sophisticated feeding apparatuses, modes of gliding locomotion, extrusive organelles, robust cell surfaces, permanently condensed chromosomes, and in some, plastids via secondary endosymbiosis. Improved knowledge of the ultrastructural diversity and phylogeny of these groups will provide the empirical foundation necessary for understanding cellular adaptation within interstitial habitats, complexity, and endosymbiosis. This research will also bring into the forefront the cellular context needed for interpreting the huge amount of genomic data being generating by different scientists around the globe, especially environmental PCR sequencing surveys of microbial diversity.

    The lab will continue to investigate the cellular diversity of meiofaunal animals, euglenids, dinoflagellates and cryomonads in order to (a) discover and characterize innovations associated with their cytoskeletons, photoreception apparatuses and feeding apparatuses; (b) provide well characterized reference taxa needed for accurate interpretations of environmental DNA surveys; and (c) understand the adaptive relationship between cytoskeletal diversity and the secondary endosymbiotic origin of photosynthesis. Because the vast majority of predatory flagellates are uncultivated and have only been minimally described with line drawings using light microscopy, there is enormous potential for ultrastructural discoveries using single-cell electron microscopy (e.g., SEM, TEM and FIB-SEM) that have implications for cell biology, developmental biology, evolutionary biology and paleontology. All of these data will be placed in a molecular phylogenetic context in order to infer trends in the evolution of cellular traits and the potential arms races that exist between single-celled predators and their prey.

    Comparative studies of single-celled eukaryotes, such as dinoflagellates, offer idiosyncratic systems for tracing the intermediate stages that gave rise to highly integrated subcellular systems. For instance, some dinoflagellates have organelles called “ocelloids” that look like the subcellular analogues to camera eyes in cephalopods and vertebrates (shown in the top row of images below); some dinoflagellates have complex extrusive organelles that look very similar to the nematocysts of cnidarians or the colloblasts of ctenophores. Our research addresses the ultrastructural and genomic diversity of many different groups of marine dinoflagellates with complex morphologies, such as dinophysoids, warnowiids and polykrikoids, resulting in a more comprehensive understanding cellular diversity.

    Dinoflagellates are ubiquitous microbial eukaryotes in both marine and freshwater environments and have very diverse ecological roles and modes of nutrition; some are predators, others are parasites of animals or symbionts of reef-building corals, and roughly half are photosynthetic. Some of the photosynthetic dinoflagellates rank among the most important players in marine primary production of carbon, whilst others are responsible for harmful (toxic) algal blooms that can negatively affect the fisheries industry, shellfish industry and public health. From the perspective of an evolutionary cell biologist, dinoflagellates are extremely interesting because they have some of the most complicated organellar systems known: the nematocyst-like extrusomes and the eye-like ocelloids. Using use a combination of approaches to study these systems, including scanning and transmission electron microscopy, FIB-SEM, isolated-organelle genomics and single-cell genomics.

    Marine gregarines (a few examples of their feeding stage are shown in the SEM images below) are a diverse and poorly understood group of single-celled parasites of invertebrate hosts and provide important insights into one of the most enigmatic evolutionary transformations in the history of life: the origin of obligate intracellular parasites from free-living, photosynthetic ancestors. Apicomplexans are a group of single-celled parasites that are closely related to dinoflagellates (described briefly in Section 2 above), and despite being infamous as pathogens of humans and livestock (e.g., Plasmodium – the causative agent of malaria), most of apicomplexan diversity is thriving in the world’s oceans. The evolutionary origin of apicomplexan parasites began within marine sediments (as described in Section 3 above); free-living relatives to apicomplexans are tiny (< 10 μm) vampire-like predators, called “colpodellids”, that feed on other microbial eukaryotes. Many marine gregarines share with colpodellids the same mode of feeding and are inferred to have retained several ancestral traits for apicomplexans as a whole (e.g., extracellular feeding stages, a lifecycle consisting of a single host and a prevailing presence in marine environments). Because of their widespread presence in animals and a long history of being overlooked by the scientific community, it is expected that the vast majority of gregarines lineages (likely in the millions) remains unknown. Very few gregarines have been examined at the ultrastructural level and only a handful of gregarines have been studied at the molecular level. Addressing this black hole of basic (correlative) knowledge is among the most ambitious components of our research program.

   The primary aims of this research section are to (a) survey the cellular and molecular diversity of marine gregarines; (b) use transcriptomics/genomics to investigate the early evolutionary history of novel organelles (e.g., apicoplasts) in apicomplexans as a whole by targeting key lineages of marine gregarines; and (c) characterize ultrastructural innovations in gregarine feeding stages with light, confocal, and electron microscopy. We have demonstrated different ultrastructural innovations and associated cell motility systems in gregarines that reflect novel solutions for cell locomotion, reproduction, host-dependent nutrition and the biological properties of specific host compartments (e.g., intestines, coeloms and reproductive vesicles). On the whole, research on poorly understood organisms, like gregarines, enhances our awareness of marine biodiversity and introduces a significant source of cellular novelty with the potential to impact more applied research. This potential is perhaps best exemplified by the unexpected discovery of apicoplasts in apicomplexans like Plasmodium and Toxoplasma, which provided a new list of novel drug targets for the treatment of malaria and toxoplasmosis.

   

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