Band 3 Researcher; Head of Division of Genomics and Microbial Diversity
Lecturer, MSc in Advanced Systematics and Taxonomy, Imperial College/NHM, and MRes in Biodiversity and Conservation, UCL/NHM
Senior Research Associate, Zoology Department, Oxford University
Vice-President, British Society for Protist Biology
2005 DPhil, Zoology Department, Oxford University
2001 MSc (Integrative Bioscience), Zoology Department, Oxford University
1999 BSc (Biological Sciences, Open University)
1993 MA (Music, The Queen's College, Oxford University)
My group works on a range of protist/microbial-related projects, with a developing emphasis of organismal interactions, parasitic protists and the ecology of disease risk.
Key projects and our collaborators are described below.
Emerging diseases are those that have appeared for the first time or may have existed previously but are rapidly increasing in incidence, severity (virulence) and geographic range. One of the main drivers of disease emergence is environmental change caused, for instance, by global warming, pollution and invasive species. Disease emergence can result as a consequence of the responses of infectious agents (parasites, pathogens) to environmental change, when invasion promotes host switching, or because of pathologies associated with exposure to toxins or other environmental contaminants. It is increasingly evident that understanding and predicting emerging diseases will require characterising and determining disease risk potential of poorly known parasites and pathogens (microbes, viruses, fungi, etc.), asymptomatic infections, and poorly understood or novel interactions (host-symbiont, vector-parasite, etc.). Another interpretation of ‘emerging’ is in terms of emerging awareness: many microbial parasites are very poorly known, often restricted to the few taxa of clear economic significance. We are interested in the broader picture, looking at parasite diversity in general and their dynamics in natural ecosystems. Some of the groups of interest are Ascetosporea and Phytomyxea (see below), ichthysporeans, labyrinthulids, Myxozoa (Cnidaria), X-cell (alveolates), parasitic variosean amoebae, and viruses.
I have a long-standing interest in the diversity, phylogeny, and ecology of Cercozoa, including ‘Endomyxa’, which includes ascetosporean and phytomyxid parasites, vampyrellid amoebae, other large amoebae, and a large diversity of lineages known only from environmental sequences. One element of this work involves using a variety of methods to determine which organisms these environmental sequences correspond to.
Phytomyxids are the sister group to vampyrellid amoebae and are parasites of of plants, algae, and oomycetes. A few species are well known, principally those causing clubroot in brassicas, powdery scab of potatoes, and those acting as vectors for plant viruses. However, recent work suggests that there is a much higher diversity of unknown phytomyxids in a wide range of habitats, which are likely to be ecologically important in diverse ways.
Ascetosporea are parasites of invertebrates, mostly marine. They include the haplosporidians, some of which are well-known (e.g. Haplosporidium nelsoni, which causes MSX disease of oysters) but most are unknown. Paradinium and relatives are currently known as parasites of copepods and prawns. Paramyxeans are parasites of shellfish, the best known example of which is Marteilia in oysters (marteiliosis). We have an active programme of research investigating diversity and distribution of many of these lineages.
Combined culture-based and molecular techniques have clarified the diversity and evolutionary relationships of many protozoan groups. However, one protozoan morphotype, the large, branched and/or net-forming heterotrophic naked amoebae, has figured only very rarely in this protozoological renaissance. These are extraordinary protists, which are often (very) large individual cells or large networks of many cell-like bodies that can cover many square centimeters of substrate. The single-celled forms can be split roughly into two behavioural types - those that adhere strongly to a surface and move only parts of the cell, generally slowly, and more mobile types that move the whole cell often quite rapidly, often with even faster pseudopodial activity. The network types are also behaviourally diverse, some with very active movement of organelles and cytoplasmic components around the network (which is sometimes itself very plastic) whereas in other strains such movement can be barely noticeable.
The NRRA morphotype is of particular interest because it suggests adaptations permitting a unique mode of occupation of a physical niche space (e.g. pervading interstitial and other very small spaces) and diverse nutritional options. NRRA are found in soils and sediments, on mosses and higher plants, and both marine and freshwater plankton where they can adopt different cell forms from their ramifying benthic state (e.g. ‘floating’ forms). They are able to feed on many prey cells at once, engulf relatively large food items, and penetrate spores, hyphae, and other cells resistant to many other kinds of attack. They are important but understudied components of suppressive soils, have many fungal prey and a wide range of mycophagous habits. NRRA are also important algal consumers, eat disease-causing worms, and affect root colonization by mycorrhizal fungi. NRRA are remarkable not only for their diversity of food sources, but often also for the rate at which this food is consumed. They eat a wide range of bacteria and eukaryotes, including many disease-causing organisms: filamentous fungi, yeasts, rusts, chytrids, tough-walled fungal spores, phytopathogenic oomycetes and other protozoa, small metazoa, and multicellular algae (including ‘seaweeds’) and plants. In the light of this information the lack of knowledge of NRRA biology and ecology may be concealing a large diversity of microbial ecosystem processes in which NRRA have unique roles, with implications for agriculture, forestry, freshwater bodies, and marine environments.
Cord-forming fungi are those that form aggregations of predominantly parallel, longitudinally-aligned hyphae. The cord-forming habit allows rapid transfer of nutrients in bulk and the ability to extend and forage between resource patches. CFF are key decomposers of dead wood litter, which represents a large reservoir of nutrients (30-40% of total biomass) unavailable to the rest of the ecosystem until released by decomposition and critical to ecosystem response to CO2 fertilisation.
Our knowledge of the phylogenetic extent of CFF is far from complete. Partly as a consequence of this, the in situ ecology of CFF distribution (i.e. substrate specificity, seasonality, etc.) is also poorly known. This is important because the phylogenetic diversity of CFF is likely to represent a functional diversity, with different taxa fulfilling different roles in the forest decomposition ecosystem. Molecular biology techniques are required to investigate this as it is difficult and in many cases impossible to distinguish between fungal cords morphologically. Research on CFF has so far focused on ecophysiology and modes of resource utlilisation, growth characteristics, and nutrient translocation. Little work has been done on the in situ diversity and ecological distribution of CFF, which are the foci of this proposal.
Predators play a major role in the evolution and ecology of diverse prey populations. While there have been numerous studies of the effect of single predators, the effect of multiple predators on diverse prey communities remains little studied. Understanding the general ecological principles that determine how predators affect prey biodiversity might be especially important for conservation biology because top predators tend to be most affected by humans. The main aim of this research is to understand the effect of predator diversity in structuring the prey community, and the repercussions for the surrounding ecosystem. Controlled experiments are virtually impossible with large organisms. The strategy that we will employ will be to investigate the effects of predators in model ecological communities composed of bacteria and their predators (protozoa).
We are also interested in protist communities in animal dung, and are currently working on a newly recognized group of cercozoan coprophiles.
The advent of next generation sequencing technologies (NGS – 454 Sequencing Illumina, etc.) means that microbial communities can be investigated more comprehensively than before, both in terms of taxonomically informative amplicons (e.g. SSU rDNA) and genome-wide surveys (metagenomics and metatranscriptomics). We are involved in a range of projects along these lines, including: