The genome of a terrestrial metazoan extremophile

Project Details

Project Lead
Luis Cunha 
Project Manager
Luis Cunha 
Institution
Cardiff University, School of Biosciences  
Discipline
Biology (603) 
Subdiscipline
02.02 Animal Sciences 

Abstract

We have massive quantity of genomic (~80x SOLID ABI) data originated from muscle tissue of an earthworm that lives in an impressive environmental within a geothermal field. Let me briefly tell you that these geothermal biotopes are reducing environments with particular unique features, such as elevated soil, water, and atmospheric elemental composition, together with constant diffuse degassing and high temperatures. “The secondary manifestations of volcanism in the geothermal field include low temperature fumaroles (maximum temperature around 100 °C), hot springs, CO2 cold springs and several diffuse degassing areas. Also the volcanic gases present in Furnas geothermal field (Azores Islands, Portugal) typically comprise water vapour, carbon dioxide (CO2), hydrogen sulfide (H2S), sulfur dioxide (SO2), hydrogen chloride (HCl), with lesser amounts of hydrogen fluoride (HF), and, the radioactive gas radon (Rn). Therefore, the ephemeral nature of the geothermal field is expected to favour the colonization by species with admirable colonization abilities” The assembly of this genome will provide an unusual opportunity to understand the dynamics thriving population structure and genetic diversity as well the integrated modifications ranging from genetic and biochemical, to cellular and physiological levels of organisation under such conspicuous environmental conditions. Now that I presented my “motivational scenario” let me tell what type of data we have. Presently our data is originated from several paired end and mate paired libraries: 100x coverage of short reads (SOLID 5500 with ECC module) 1x Single fragment (75 bp) (with ECC) 2x Paired end (~160-200 bp) 2x Mate pair (500bp-1kb) (with ECC) 1x Mate pair (3-5kb) (with ECC) In theory the denovo task that I am undertaken is far from easy but I believe that with your computing power we could go a bit further. I must say that our aim is to get as much as possible genetic units from this genome, although large contigs would be a great achievement but for that we need several core processor and as much RAM as we can get. These are very intensive computing jobs and I am having difficulties in finding the proper resources.

Intellectual Merit

This project represents the interaction between the geochemistry of active volcanic soil (constant diffuse degassing, high temperature and elevated metal ion availability), and the biology of the organisms that are intimate contact with this environment. The project will use targeted techniques to investigate the ecophysiology of the organism as it pertains to its O2 consumption, underlying metabolism and metallo-biology. These targeted investigations will be complemented by exploiting global studies using functional and phylogenetic molecular approaches refined and optimised in previous projects whilst studying the temperate sentinel earthworm, L. rubellus. These molecular tools kit will allow us to unlock the mechanistic changes associated with each stressor; hypoxia/hypercapnia, elevated temperature and increased metal availability, individually and in concert. Through a linked PhD studentship, we will be able to use a complementary set of genetic tools to characterize global and local context of the population resident to the active volcanic soils. Of specific focus will be the implication of this species’s reproductive strategy, reported to be predominately parthenogenetic, for invasion and adaptation at a global landscape level and to specific micro-habitats. Thus, the proposed project is of necessity interdisciplinary; this being reflected in the spectrum of expertise represented by the project team, which includes a geochemist (Prof. Mark Hodson), an earthworm biologist (Prof. A. John Morgan), a population geneticist (Prof. Mike. Bruford), and a molecular biologist (Dr Peter Kille). [In addition, we shall collaborate with an ecotoxicologist and a vulcanologist at the University of the Azores, and an earthworm taxonomist who will sample throughout Asia (Laos, Korea, Thailand, South China)]. This body of expertise will be supplemented by the NERC molecular facilities at Edinburgh (NBAF-E) to ensure that the cutting edge ‘omic technologies are deployed effectively and economically. Each member of the team represents a discrete community that will benefit from knowledge generated by the project. The findings will benefit a number of specific additional academic communities, including: earthworm ecologists studying dispersal and colonisation of island habitats; those studying the contribution of earthworms to pedogenesis and above-ground/below-ground interactive processes on volcanic islands; those investigators considering the molecular-genetic dimension of the adaptation of invertebrates to hypoxia, hypercapnia, temperature and elevated metal ion concentrations; those studying the interaction between these stressors either in natural environmentally, under laboratory-controlled experimental conditions, or under clinical conditions (e.g. hypoxia, ischemia); those currently using A. gracilis as the preferred vermicomposting species in tropical climates; those seeking to extend sustainable forms of agricultural activities by reclaiming or exploiting certain land areas currently considered marginal. Finally, genetic and genomic resources arising from the project will almost certainly establish A. gracilis as a prime pan-tropical sentinel organism for terrestrial biomonitoring applications. A specific beneficiary we are targeting is the collaborative research group on the Azores who will receive both training and genetic resources enabling them to expand their research capability in this remarkable environment. Moreover, we shall collectively explore the possibility of miniaturizing and data-logging the field-based soil-gases measurements, so that the technology becomes more portable and of broader applicability. Finally, through established network of International Symposia of Earthworm Ecology we shall increase the awareness and engagement of local and international stakeholders.

Broader Impacts

The direct beneficiaries of this research will be government organizations involved in managing active volcanic sites, both in the specific location under investigation, the Furnas caldera on Sao Miguel (Azores), but also with implications for volcanic regions across the globe. The molecular-genetic outputs will provide the basis for developing earthworm-based diagnostic monitoring tools for informing human and environmental risk assessment of active volcanic soils. Significant technology transfer will benefit the local research community within the Azores, providing them with a completely new genetic ‘tool box’ which may be applied to better understand the local ecosystem, how it was established, and the ongoing interactions between the geochemistry of the volcanic soils and the island’s biota. The widest community to benefit will be those organizations involved in the management of circum-tropical terrestrial environments. The cosmopolitan distribution of the target organism, the megascoelecid earthworm A. gracilis, in warm climates provides it with the potential to be a sentinel for in situ terrestrial biomonitoring in ways that are analogous to those developed in temperate zones for the lumbricid earthworm Lumbricus rubellus. Since the distribution of invasive A. gracilis encompasses many countries where mining and manufacturing industries are at present poorly regulated, there will be an increasing future requirement for robust ecotoxicological evaluation and management of these contaminated terrestrial habitats. Other communities will potentially benefit through secondary conduits such as academic medical researchers investigating conditions such as metabolic abnormalities, hypoxia (e.g. ischemia), hypercapnia, and dysfunctions of metal metabolism. Since this research proposal will probe the basic biochemical pathways involved in these processes, and since many of the biological processes involved are evolutionarily conserved, the data generated will be directly transferable to related clinical research fields. Furthermore, the research will provide valuable insight into temperature adaptation and island colonization (specifically to parthenogenesis as an evolutionary strategy) and, in turn, this will inform climate change and colonization/invasion modelling. The team is passionate about the widest possible engagement for its research, both to the general public and to the wider student (undergraduate and sixth form) fraternity. The team has a significant history of community engagement through articles (‘Heavy Metal-Eating "Superworms”’ Hodson, ME – National Geographic News, Oct 7, 2008), participatory activities (‘Wales Worm Watch’; ‘The Wonderful World of Worms’ – Kille, P. and Morgan, A.J.), and films (‘Sentinel Animals: Soil Pollution’, 2008) in addition to engagement activities such as Science Week, nstitutional Open Days, and School visits. All team members will use the research to inform teaching generally and in undergraduate and MSc projects. These activities are considered routine; therefore, we will not assign specific resources to them in our “pathway to impact” plan. 2. Methods of engagement: What activities will be performed to underpin impact? To ensure transparency and to facilitate public engagement the team will host a web site using an “interactive wiki” component that will not only allow project objectives and results to be presented but will also allow interactive discussion of key aspects of the work. The project benefits greatly from its close collaboration with the University of the Azores (UoA) (Department of Biology, and the Centre for Volcanology & Geological Risk Assessment). These academic groups are the primary advisors to their Local Government Agencies relating to the interaction and management of the active volcanic sites and the local ecology and human habitation. Therefore, we are confident that fostering this interaction will deliver local governance benefits. There has been significant prior engagement with the University of the Azores, as evidenced by their supporting letters, and we will continue this close interaction throughout the project. We will consolidate this interaction by organizing small local symposia during the two scheduled field sampling expeditions, together with an “impact meeting” scheduled at the termination of the project to present our research findings. Technology transfer to the collaborators on the Azores will be achieved by an explicit research exchange allowing Mr Luis Cunha to visit Cardiff and undergo two months research in Years 2 and 3 of the project. The objective will be to provide Mr Cunha with training in the molecular-genetic and informatic approaches being employed within the grant and to transfer this knowledge tohis collegues at the UoA. Engaging a wider distributed community, such as those involved in environmental monitoring in pantropical regions of the globe, is a complex and challenging task. A component of the research team’s normal activities will be to present the data at international meetings of the Society of Environmental Toxicology and Chemistry (SETAC), whose mission is to target a global regulatory audience, as well as to forge specific ties to groups such as the Organisation for Economic Co-operation and Development (OECD) with a global remit in sustainable environmental development. We will specifically target Asia/Pacific SETAC meetings to ensure that the research reaches an appropriate audience. Furthermore, the PI and CoI are extremely active in the international community, with PK having acted as an advisor to the OECD and is part of an ongoing programme looking at exploiting molecular advances to underpin environment diagnostics. MWB also advises many organizations and governments on conservation issues. However, to maximize the delivery of impact we will engage with Cardiff’s ‘Sustainable Places Research Institute’ (http://www.cardiff.ac.uk/research/sustainableplaces/) to ensure the widest dissemination of the research findings. To ensure the widest possible impact through secondary academic endeavours, such as medical research and environmental modelling, open access rights will be obtained for all publications streaming from this research. Furthermore, the group will continue its policy (already established in ECOWORM and SEQAWORM projects) of online disclosure through the LumbriBASE portal of genetic data as it is generated.

Scale of Use

I would like to run several genome assemblies that may escalate to a bit more than 500Gb of RAM and 1.5TB of storing space. I will be managing resources wisely.

Results

The complete genome of Pontoscolex corethrurus