Ecological and morphological characterisation, and phylogeny of Endomyxa: poorly known but widespread and diverse protozoan parasites and omnivores
Lead Research Organisation:
Natural History Museum
Department Name: Life Sciences
Abstract
Endomyxa are a very poorly known but large and diverse group of organisms in the protozoan phylum Cercozoa. Endomyxa includes the commercially important plasmodiophorid plant parasites, and haplosporidia and relatives, which include parasites of a wide range of invertebrates, most famously MSX disease of oysters. The evolutionary relationships of both of these groups were for a long time unknown (plasmodiophorids were considered fungi for a long time), but good ribosomal DNA trees show that they are related to each other (a relationship reinforced by morphological synapomorphies) and several lines of molecular evidence show that they belong within the eukaryotic supergroup Rhizaria, specifically as a subphylum within Cercozoa, but separately from the so-called 'core' Cercozoa. More recently, free-living relatives of these parasites have been found through culturing/cell isolation and rDNA sequencing. These include the large testate marine filose amoeba Gromia, and large reticulose, naked amoebae: the bacterivorous Filoreta and the predatory Arachnula and Platyreta. Such organisms represent very distinct and poorly studied protozoan morphotypes whose ecological roles are almost completely unknown. Other research has revealed more endomyxan parasites, for example the spot prawn parasite, and Paradinium, a parasite of copepods. Culture-independent environmental rDNA libraries show that there are a large diversity of other endomyxan clades and lineages which remain uncharacterised - the only information we have for them is the provenance of the samples in which the sequences were detected. The environmental libraries also show that there is very strong ecological structuring - many endomyxan clades have so far only been found in quite specific habitats, for example deep-sea samples, anaerobic marine, anaerobic freshwater, or phylloplane communities. These patterns suggest high levels of ecological specialization, perhaps involving interactions with other organisms. This project aims to identify as many of these novel lineages and clades as possible, whether they are free-living, symbiotic, or parasitic, using a combination of intensive selective culturing using a diversity of food sources and culture conditions informed by the results of the environmental libraries, and fluorescent in situ hybridization (FISH) using fluorescent probes that will specifically detect chosen uncharacterized lineages. FISH will also show the relative abundance of endomyxan lineages in different habitats, and whether they are associated with, or are found inside, other eukaryote cells, and if so, which organisms they co-occur with (and are therefore perhaps parasites of). Multiple and diverse SSU rDNA environmental libraries will be constructed, using a set of overlapping PCR primers covering all Endomyxa, to show much more clearly and realistically than previously possible the true diversity of Endomyxa, and their ecological nature by analyzing the sequence data in the context of other biotic and abiotic variables co-measured at each sampling site. The libraries will be made using both rDNA and crDNA reverse transcribed from rRNA: the latter is generally taken as a surrogate for the level of activity of the cells (more ribosomes will be present in more active cells), rather than just presence/absence and biomass as indicated by rDNA. This approach will provide more informative about the ecological characteristics than rDNA libraries alone. The environmental sequences will be used to improve phylogenetic reconstructions of Endomyxa and their relationships to the rest of Rhizaria both by increasing taxon sampling of this part of the tree, and by providing sequence data that can be used to obtain LSU rDNA sequences for representative genotypes directly from environmental DNA samples. Where cultures are available, other genes can be targeted by PCR, to be combined with existing data in multigene phylogenies.
Organisations
- Natural History Museum (Lead Research Organisation)
- National Center for Scientific Research (Centre National de la Recherche Scientifique CNRS) (Collaboration)
- CENTRE FOR ENVIRONMENT, FISHERIES AND AQUACULTURE SCIENCE (Collaboration)
- Rothamsted Research (Collaboration)
- University of Oslo (Collaboration)
- University of Warwick (Collaboration)
- Spanish National Research Council (Project Partner)
- TU Kaiserlautern (Project Partner)
- Smithsonian Tropical Research Institute (Project Partner)
- NERC CEH (Up to 30.11.2019) (Project Partner)
People |
ORCID iD |
David Bass (Principal Investigator) |
Publications
Hartikainen H
(2014)
Mikrocytids are a broadly distributed and divergent radiation of parasites in aquatic invertebrates.
in Current biology : CB
Logares R
(2014)
Patterns of rare and abundant marine microbial eukaryotes.
in Current biology : CB
Massana R
(2015)
Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing.
in Environmental microbiology
Stentiford GD
(2015)
Paradoxium irvingi n.gen. n.sp. (Microsporidia) infecting the musculature of European pink shrimp Pandalus montagui.
in Journal of invertebrate pathology
Bass D
(2015)
Diverse Applications of Environmental DNA Methods in Parasitology.
in Trends in parasitology
Van Wichelen Jeroen
(2016)
A Hotspot of Amoebae Diversity: 8 New Naked Amoebae Associated with the Planktonic Bloom-forming Cyanobacterium
Microcystis
in ACTA PROTOZOOLOGICA
Ploch S
(2016)
High Diversity Revealed in Leaf-Associated Protists (Rhizaria: Cercozoa) of Brassicaceae.
in The Journal of eukaryotic microbiology
Friman VP
(2016)
Relative importance of evolutionary dynamics depends on the composition of microbial predator-prey community.
in The ISME journal
Title | Black Box Safari |
Description | An art installation in Oxfordshire where members of the public were offered a self-guided tour (safari) where black boxes were distributed around the site. Each box had a magnifying glass attached to the top of the box, which invited insepction. On looking through the glass, viewers see a loop video showing eukaryotic microbes filmed from samples taken from the same site. |
Type Of Art | Artistic/Creative Exhibition |
Year Produced | 2011 |
Impact | Many discussions on microbial biology, eukaryotic evolution, the interaction of art an science, and the roles of scientists in society. An extremely and often unexpectedly productive and rewarding set of interactions. |
Description | 1. Demonstration and analysis of large diversity of Endomyxa in many globally distributed locations and the majority of habitat types. 2. Reconstruction of the endomyxan evolutionary tree, showing how different body forms, lifestyles (e.g. parasitism, predation, large body size) have evolved and from which ancestors. 3) Description of new endomyxan taxa (species and above), including both parasites and free-living organisms. 4) Discovery and characterisation of a major new group of parasites - the mikrocytids - which cause serious diseases of crabs and bivalve molluscs that impact the fishing industry, and demonstration that these parasites are diverse and sometimes abundant in a wide range of hosts in both marine and non-marine habitats. 5) Discovery of previously hidden diversity of plasmodiophorid plant parasites and their relatives that parasitise many marine algae, seaweeds, and seagrasses. Our analyses showed very wide variation in host taxa for these parasites, suggesting their general occurrence and importance. 6) Unveiling of large diversity of vampire amoebae (vampyrellids) including many new lineages and new species in marine habitats, where they were previously almost unknown. 7) Development of environmental DNA methods for detecting and discovering microbial diversity and understanding its ecology without having to sample or culture individual cells, which is time consuming, expensive, and scientifically biased. |
Exploitation Route | Our findings on parasites are being integrated into work on shellfish of food security interest, both in terms of understanding diseases of these food organisms and how fisheries may be sited to avoid such diseases, and also methods of detecting parasites and pathogens in environmental samples. The latter is potentially very powerful as it makes sampling less biased, higher throughput, and therefore more efficient and less expensive, but has a requirement for specificity that is informed by our findings about high levels of diversity of these parasites in many habitats. |
Sectors | Aerospace, Defence and Marine,Agriculture, Food and Drink,Education,Environment,Government, Democracy and Justice |
Description | Discoveries of novel parasitic taxa and diversity are currently being used in a food security context - i.e. in understanding the role of these novel parasites and diversity of pathogens is a) directly affecting shellfish health and survival, and b) methods of monitoring disease risk and occurence and policies related to those activities, including many developments of eDNA methods. |
First Year Of Impact | 2012 |
Sector | Aerospace, Defence and Marine,Agriculture, Food and Drink,Education,Environment,Government, Democracy and Justice,Culture, Heritage, Museums and Collections |
Impact Types | Cultural,Economic,Policy & public services |
Description | Parasite diversity and distribution |
Geographic Reach | National |
Policy Influence Type | Influenced training of practitioners or researchers |
Description | Systematics in parasitology |
Geographic Reach | Europe |
Policy Influence Type | Influenced training of practitioners or researchers |
Description | BBSRC CCC Scheme |
Amount | £12,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start |
Description | BBSRC Newton Fund GRP |
Amount | £1,900,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2016 |
End | 02/2019 |
Description | BBSRC SARISA 2014 |
Amount | £30,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2014 |
End | 09/2018 |
Description | Defra research and development project |
Amount | £546,480 (GBP) |
Organisation | Department For Environment, Food And Rural Affairs (DEFRA) |
Sector | Public |
Country | United Kingdom |
Start | 03/2017 |
End | 03/2020 |
Description | H2020-SFS-2015-2 |
Amount | € 449,000 (EUR) |
Organisation | European Commission |
Sector | Public |
Country | European Union (EU) |
Start | 03/2016 |
End | 03/2020 |
Description | NERC Freshwater Highlight topic |
Amount | £552,000 (GBP) |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 03/2016 |
End | 04/2020 |
Description | Research Project |
Amount | £750,000 (GBP) |
Organisation | Department For Environment, Food And Rural Affairs (DEFRA) |
Sector | Public |
Country | United Kingdom |
Start | 03/2015 |
End | 03/2018 |
Description | SynTax (Phytomyxids) |
Amount | £19,845 (GBP) |
Organisation | Linnean Society of London |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | |
End | 12/2014 |
Description | SynTax (parasites) |
Amount | £29,000 (GBP) |
Organisation | Linnean Society of London |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 04/2013 |
End | 02/2014 |
Title | Parasite environmental detection and non-invasive infection status assessment by eDNA |
Description | The use of eDNA methods (nucleic acid extraction from environmental or organismal matrix following by sequencing either via general or specific PCR primers or by metagenome/transcriptome sequencing) has been shown to be a powerful method for measuring microbial (including parasite) diversity and distribution in situ. We have refined these sampling and processing methods for eukaryotic aquatic parasites, reported in several papers, and others in prep. Additionally, we have developed and are refining non-invasive eDNA-based methods for detecting and monitoring disease status of shellfish and finfish for use in aqaculture and wild capture fisheries research and monitoring. |
Type Of Material | Biological samples |
Year Produced | 2012 |
Provided To Others? | Yes |
Impact | Academic publications, (pending) adoption of sampling and processing methods into workflow of relevant practitioners (e.g; Cefas, Environment Agency, JNCC). See details of workshop delivery to JNCC in other section of this form. Similar delivery to Cefas. |
Title | Cefas collections |
Description | Cefas maintains collections of parasite(-related) material. Much of the parasite work as part of the Endomyxa NERC award was done in collaboration with Cefas, resulting in their adding histology slides, EM preps, and fixed specimens for further analysis to their collections. These correspond to crustean, mollusc, and annelid hosts, and a range of microbial eukaryotic parasites, mostly ascetosporeans (Endomyxa). |
Type Of Material | Database/Collection of data |
Year Produced | 2013 |
Provided To Others? | Yes |
Impact | The edible crab materials for Paramikrocytos canceri, a newly described mikrocytid crab pathogen have been used in a Current Biology (2014) paper on this organism and other mikrocytids, and have been made available to other researchers collaborating with us on mikrocytid genomics. The collections will also be used by national reference laboratories across Europe (EURLs), within which Cefas is the crustacean representative. |
Title | Protist culture collections |
Description | Protist strains isolated and named were deposited in several international culture collections - CCAP, ATCC, NIES |
Type Of Material | Database/Collection of data |
Year Produced | 2010 |
Provided To Others? | Yes |
Impact | Protist strains provided directly to other researchers for taxonomic, ecological, and cell biology studies and publications. Making these available also via publically-accessible culture collections. |
Description | BioMarKs |
Organisation | National Center for Scientific Research (Centre National de la Recherche Scientifique CNRS) |
Department | Biological Station, Roscoff |
Country | France |
Sector | Academic/University |
PI Contribution | Contribution to sampling and processing of samples and data. Specific scientific input regarding Cercozoa (including Endomyxa) diversity analyses, phylogenetics, and interpretation. |
Collaborator Contribution | Covering the cost for and carrying out 1.5 plates of 454 sequencing to investigate endomxyan diversity in marine sample. Data generated, analyses ongoing. |
Impact | Publications listed in relevant section. Contribution to seminars and scientific meetings connected with this collaboration. Other aspects of work in progress. |
Start Year | 2009 |
Description | Cefas |
Organisation | Centre For Environment, Fisheries And Aquaculture Science |
Country | United Kingdom |
Sector | Public |
PI Contribution | Expertise in molecular protistology, eDNA methods, and phylogenetics, contributing to a balanced collaboration. |
Collaborator Contribution | Expertise in pathology, parasitology, and associated microscopy, contributing to a balanced collaboration. |
Impact | Several publications on protistan parasites - see publications section. Also student co-supervision, including a NERC DTP (GW4+) studentship with Exeter and The Natural History Museum, starting September 2014. The collaboration is multi-disciplinary, involving next generation sequencing, eDNA, phylogenetics, parasitology, pathology, histology, electronc microscopy, and policy engagement. |
Start Year | 2011 |
Description | Collaboration with Oslo University |
Organisation | University of Oslo |
Country | Norway |
Sector | Academic/University |
PI Contribution | Heavy contribution to funding proposal to Research Council of Norway on X-cell (alveolates) parasites of fish, and subsequent meetings, collaboration, analyses, paper writing, etc. |
Collaborator Contribution | Managing funded grant, collaboration, next generation sequencing (amplicon and metagenomics), analyses, paper writing, etc. |
Impact | Large sequence datasets generated from fish and invertebrate hosts, environmental samples, etc. - both amplicon and metagenomics libraries. Publications in preparation. |
Start Year | 2011 |
Description | NERC PhD Studentship, Warwick |
Organisation | University of Warwick |
Department | School of Life Sciences |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | David Bass devised as is co-supervisor on a NERC-funded CASE PhD studentship held at Warwick School of Life Science, with NHM as CASE partner. The project is on plasmodophorid plant parasites. DB's contributed is training and supervision relating to this particular group of protists (belonging to Endomyxa), molecular phylogenetics, bioinformatics, microbial ecology, and eDNA methods. The NHM also co-funds the studentship (stipend and scientific costs). |
Collaborator Contribution | Warwick hosts the student, provides expertise on soil ecology and plant-soil-microbe interactions, and statistics. |
Impact | Training of PhD student to delivery of PhD thesis (due in 2015), papers in preparation. |
Start Year | 2011 |
Description | Rothamsted Research |
Organisation | Rothamsted Research |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Data analysis for soil metatranscriptome project and sequencing costs for soil disease suppressivity experiments. |
Collaborator Contribution | Large scale soil transcriptome data analysis (in partnership with TGAC Norwich), and provision of samples for this project and disease suppressivity project. Several papers in preparation. |
Impact | Collaboration and publications in preparation |
Start Year | 2011 |
Description | August 2019: Past President's Plenary address at ISoP, Rome |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Plenary presentation at the annual meeting of the International Society of Protistologists, in role of Past President |
Year(s) Of Engagement Activity | 2019 |
Description | Co-organiser and plenary presenter, ARCH-UK Microbiome Workshop, Aberdeen |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | Workshop as part of ARCH-UK NERC/BBSRC Aquaculture initiative. Presentation on microbiomes followed by discussions, session chairing, and workshop leading. |
Year(s) Of Engagement Activity | 2018 |
Description | February 2019: Invited seminar, Oslo University |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | Research presentation with collaborators and wider audience in Oslo University Biosciences department |
Year(s) Of Engagement Activity | 2019 |
Description | Filming for BBC |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Interview for BBC4 programme (Nature's Weirdest) on use of next generation sequencing methods for biological discovery and characterisation, based on methods (metagenomic sequencing) used in both NERC grants. Programme to air in January 2015 so no further impact yet. |
Year(s) Of Engagement Activity | 2014 |
Description | Invited plenary speaker at Czech Society for Parasitology meeting, Czech Republic |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Plenary talk at parasitology conference followed by discussions. |
Year(s) Of Engagement Activity | 2018 |
Description | Invited plenary speaker at Society for Experimental Biology meeting, Azores |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited presentation at conference focussing on effects of high CO2 levels on microbes and influencing animal disease in the oceans. |
Year(s) Of Engagement Activity | 2018 |
Description | Invited seminar, Oslo University |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | Presentation to collaborators and other faculty members in the biosciences department of Oslo University. Approx 40 attendees. |
Year(s) Of Engagement Activity | 2019 |
Description | March 2019: Symposium chair: eDNA, ecology and environment, World Aquaculture Society meeting, New Orleans |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Talks and workshops in eDNA and parasites/diseases of aquatic animals given at World Aquaculture Society conference |
Year(s) Of Engagement Activity | 2019 |
Description | Postgraduate teaching |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Teaching postgraduates about microbial biodiversity and evolution, and next generation sequencing technologies and applications. Also parasite-host interactions and parasite ecology. Discussion, MSc, MRes, and PhD project students, publications, requests for advice and assistance. |
Year(s) Of Engagement Activity | 2010,2011,2012,2013,2014 |
Description | School talk - Kingsbridge Community College |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Talk to school students (GCSE to A level) on symbiosis and parasitism. Subsequent delivery of annotated slides and follow-up contact/advice. |
Year(s) Of Engagement Activity | 2015 |
Description | Schools talks |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Talk to GSCE and A level students followed by questions and discussion, and more generally on career progression and choices in science. Post-talk discussion, work placement students |
Year(s) Of Engagement Activity | 2012,2013,2014 |
Description | Science Uncovered 2016 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Science Uncovered event at The Natural History Museum (NHM), attended by c. 10,000 people - part of European Researchers' Night (EU funded). Showcasing the science and research at NHM. I contributed to two stalls - one of microeukaryotic diversity, the other on the SARISA (BBSRC) Roots of Decline project. |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.nhm.ac.uk/visit/exhibitions/science-uncovered-2016.html |
Description | Science Uncovered, NHM |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Science Uncovered at The Natural History Museum, and other public engagement events at NHM. Demonstration and discussion of work relating to these grants and more broadly. Lab visits, discussion, student placements, requests for advice. |
Year(s) Of Engagement Activity | 2011,2012,2013 |
Description | Symposium chair: eDNA, ecology and environment, World Aquaculture Society meeting New Orleans |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | 40 people in symposium (eDNA, ecology and environment, World Aquaculture Society meeting, New Orleans). 5 talks followed by discussion and information sharing. |
Year(s) Of Engagement Activity | 2019 |
Description | Talk to Fleet Study Group |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | Talk given on microbiakl eukaryote diversity and role of parasites to the Fleet Study Group, Weymouth, in relation to their conservation and management work on Chesil Beach and the Fleet lagoon. Requests for advice re. eDNA methods, questions about the science presented, interest in future collaboration/consultancy. |
Year(s) Of Engagement Activity | 2013 |
Description | VIVALDI H2020 bivalve health project conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Plenary presentation and session coordination for EU-funded bivalve health and disease mitigation project. |
Year(s) Of Engagement Activity | 2019 |
URL | https://www.vivaldi-project.eu/ |
Description | Workshop for JNCC |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Invited workshop on eDNA methods to staff/practitioners at JNCC. Devised and presented by David Bass and Hanna Hartikainen (worked on Endomyxa NERC grant). Seminars and workshop exercises. Presentation of materials to JNCC following the 1-day event. Greatly increased understanding of these molecular methods by JNCC staff and discussion about how they could be applied. Ongoing integration and development of eDNA methods into JNCC work. |
Year(s) Of Engagement Activity | 2014 |
Description | eDNA in Parasitology workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | workshop on the use of Edna (environmental DNA) methods in parasitology and policy development. |
Year(s) Of Engagement Activity | 2015 |