Dr David Bass

David Bass
  • Researcher, Head of Division
  • Life Sciences department
  • Genomics and Microbial Biodiversity Division
Natural History Museum
Cromwell Road
London
SW7 5BD

Biography

Positions

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

Qualifications

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)

Research

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.

Microbial parasites and emerging diseases

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.

Cercozoa and Endomyxa

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. 

  • Sigrid Neuhauser  currently holds a Schroedinger Fellowship to work with my group on investigating phytomyxid diversity, ecology, and host range and interactions. 
  • Serena Thomson, a NERC CASE PhD student co-supervised with Gary Bending is working on phytomyxid ecology in soils and agricultural systems. 
  • The role of phytomyxids in plant community structure forms part of Chris Jeffs’s PhD project, co-supervised with Owen Lewis.

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. 

  • Hanna Hartikainen
  • Charlotte Wood, MSc student
  • Georgia Ward, MSc student
  • Collaborating with CEFAS, Weymouth

Biodiversity, phylogeny, and ecology of large naked ramose/reticulose amoebae (NRRA)

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.

Diversity and substrate specificity of cord-forming fungi (CFF) in native and non-native UK woodlands

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.

Microbial Ecology

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.

Environmental metagenomics and metatranscriptomics

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:

Publications

2013
  • Berney C, Romac S, Mahé F, Santini S, Siano R, Bass D. ( 2013 ) Vampires in the oceans: predatory cercozoan amoebae in marine habitats. ISME in press : .
  • Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, Boutte C, Burgaud G, de Vargas C, Decelle J, Del Campo J, Dolan JR, Dunthorn M, Edvardsen B, Holzmann M, Kooistra WH, Lara E, Le Bescot N, Logares R, Mahé F, Massana R, Montresor M, Morard R, Not F, Pawlowski J, Probert I, Sauvadet AL, Siano R, Stoeck T, Vaulot D, Zimmermann P, Christen R. ( 2013 ) The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Research (Database issue) 41 : D597-604 . doi:10.1093/nar/gks1160
  • Hartikainen H, Ashford OS, Berney C, Okamura B, Feist SW, Baker-Austin C, Stentiford GD, Bass D ( 2013 ) Lineage-specific molecular probing reveals novel diversity and ecological partitioning of haplosporidians. ISME in press : .
  • Simek K, Kasalický V, Jezbera J, Horňák K, Nedoma J, Hahn MW, Bass D, Jost S, Boenigk J. ( 2013 ) Differential freshwater flagellate community response to bacterial food quality with a focus on Limnohabitans bacteria. ISME . doi:10.1038/ismej.2013.57
2012
  • Adl SM, Simpson AG, Lane CE, Lukeš J, Bass D, Bowser SS, Brown MW, Burki F, Dunthorn M, Hampl V, Heiss A, Hoppenrath M, Lara E, Le Gall L, Lynn DH, McManus H, Mitchell EA, Mozley-Stanridge SE, Parfrey LW, Pawlowski J, Rueckert S, Shadwick L, Schoch CL, Smirnov A, Spiegel FW. ( 2012 ) The revised classification of eukaryotes. Journal of Eukaryotic Microbiolology 59(5) : 429-93 . doi:10.1111/j.1550-7408.2012.00644.x.
  • Bass D, Yabuki A, Santini S, Romac S, Berney C. ( 2012 ) Reticulamoeba is a long-branched Granofilosean that is missing from sequence databases. PLos One 7(12) : e49090 . doi:10.1371/journal.pone.0049090
  • Boenigk J, Ereshefsky M, Kerstin Hoef-Emden K, Mallet J, Bass D. ( 2012 ) Concepts in protistology: species definitions and boundaries. European Journal of Protistology 48 : 96-102 . doi:10.1016/j.ejop.2011.11.004
  • Pawlowski J, Audic S, Adl S, Bass D, Belbahri L, Berney C, Bowser SS, Cepicka I, Decelle J, Dunthorn M, Fiore-Donno AM, Gile GH, Holzmann M, Jahn R, Jirků M, Keeling PJ, Kostka M, Kudryavtsev A, Lara E, Lukeš J, Mann DG, Mitchell EA, Nitsche F, Romeralo M, Saunders GW, Simpson AG, Smirnov AV, Spouge JL, Stern RF, Stoeck T, Zimmermann J, Schindel D, de Vargas C. ( 2012 ) CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biology 10(11) : e1001419 . doi:10.1371/journal.pbio.1001419
  • Richards TA, Jones MDM, Leonard G, Bass D. ( 2012 ) Marine fungi: their ecology and molecular diversity. Annual Review of Marine Science 4 : 495-522 . doi:10.1146/annurev-marine-120710-100802
2011
  • Bass D, Richards TA. ( 2011 ) Three reasons to re-evaluate fungal diversity ‘on Earth and in the ocean’. Fungal Biology Reviews 25 : 159-164 . doi:10.1016/j.fbr.2011.10.003
  • Glücksman E, Snell EA, Berney C, Chao EE, Bass D, Cavalier-Smith T (2010) ( 2011 ) The Novel Marine Gliding Zooflagellate Genus Mantamonas (Mantamonadida ord. n.: Apusozoa). Protist 162 : 207-221 . doi:10.1016/j.protis.2010.06.004
  • Howe AT, Bass D, Chao EE, Cavalier-Smith T. ( 2011 ) New genera, species, and improved phylogeny of Glissomonadida (Cercozoa). Protist 162 (5) : 710-722 . doi:10.1016/j.protis.2011.06.002
  • Howe AT, Bass D, Scoble J, Lewis L, Vickerman K, Arndt H, Cavalier-Smith T. ( 2011 ) Novel cultured protists identify deep-branching environmental DNA clades of Cercozoa: new genera Tremula, Micrometopion, Minimassisteria, Nudifila, Peregrinia. Protist 162 : 332-372 . doi:10.1016/j.protis.2010.10.002
  • Jones MDM, Forn I, Gadhela C, Egan MJ, Bass D, Massana R, Richards TA. ( 2011 )  Discovery of novel intermediate forms redefines the fungal tree of life. Nature 474 : 200-3 . doi:10.1038/nature09984
  • Jones MDM, Richards TA, Hawksworth DL, Bass D. ( 2011 ) Validation and justification of the phylum name Cryptomycota phyl. nov. IMA Fungus 2 : 173-175 . doi:10.5598/imafungus.2011.02.02.08
2010
  • Bass D, Boenigk J. ( 2010 ) Everything is Everywhere: a 21st Century De-/Reconstruction. Ed. D Fontaneto), In: Systematics Association Special Volume: Biogeography of Microscopic Organisms: Is Everything Everywhere? . The Systematics Association, Cambridge University Press : Cambridge , 88-110 .
  • Glücksman E, Bell T, Griffiths RI, Bass D. ( 2010 ) Closely related protist strains have different grazing impacts on natural bacterial communities. Environmental Microbiology 12 : 3105-3113 . doi:10.1111/j.1462-2920.2010.02283.x
  • Stoeck T, Bass D, Nebel M, Christen R, Jones MDM, Breiner H-W, Richards TA ( 2010 ) Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Molecular Ecology 19(s1) : 21-31 . doi:10.1111/j.1365-294X.2009.04480.x
2009
  • Bass D, Brown N, Mackenzie-Dodds J, Dyal P, Nierzwicki-Bauer S, Vepritskiy AA, Richards TA. ( 2009 ) A molecular perspective on protozoan biogeography and ecological differentiation using cyclotrichiids as a model group. Journal of Eukaryotic Microbiology 56 : 559-567 . doi:10.1111/j.1550-7408.2009.00434.x
  • Bass D, Chao E-Y, Nikolaev S, Yabuki A, Ishida K-I, Berney C, Pakzad U, Wylezich C, Cavalier-Smith T. ( 2009 ) Phylogeny of novel naked filose and reticulose Cercozoa: Granofilosea cl. n. and Proteomyxidea revised. Protist 160 : 75-109 . doi:10.1016/j.protis.2008.07.002
  • Bass D, Howe AT, Mylnikov AP, Vickerman K, Chao EE-Y, Edwards Smallbone J, Snell J, Cabral Jr C, Cavalier-Smith T. ( 2009 ) Phylogeny and classification of Cercomonadida: Cercomonas, Eocercomonas, Paracercomonas, and Cavernomonas gen. n. Protist 160 : 483-521 . doi:10.1016/j.protis.2008.07.002
  • Cavalier-Smith T, Oates B, Lewis R, Chao EE, Bass D. ( 2009 ) Helkesimastix marina n. sp. (Cercozoa: Sainouroidea superfam. n.) a gliding zooflagellate of novel ultrastructure and unusual ciliary behaviour. Protist 160 : 452-479 . doi:10.1016/j.protis.2009.03.003
2008
  • Cavalier-Smith T, Lewis R, Chao EE, Oates B, Bass D. ( 2008 ) Morphology and phylogeny of Sainouron acronematica sp. n. and the ultrastructural unity of Cercozoa. Protist 159 : 591-620 . doi:10.1016/j.protis.2008.04.002
2007
  • Adl SM, Leander BS, Simpson AGB, Archibald  JM, Anderson OR, Bass D, Bowser SS, Brugerolle G, Farmer MA, Karpov SA, Kolisko M, Lane CE, Lodge DJ, Mann DG, Meisterfeld R, Mendoza L, Moestrup O, Mozley-Standridge SE, Smirnov AV, Spiegel F. ( 2007 ) Diversity, nomenclature, and taxonomy of protists. Systematic Biology 56 : 684-689 . doi:10.1080/10635150701494127
  • Bass D, Howe AT, Barton H, Brown N, Demidova M, Michelle H, Li L, Sanders H, Watkinson SC, Willcock S, Richards TA. ( 2007 ) Yeast forms dominate fungal diversity in the deep oceans. Proc Roy Soc B 274 : 3069-3077 .
  • Bass D, Richards TA, Matthai L, Marsh V, Cavalier-Smith T. ( 2007 ) DNA evidence for global dispersal and probable endemicity of protozoa. BMC Evolutionary Biology 7 : 16 . doi:10.1186/1471-2148-7-162
  • Moreira D, von der Heyden S, Bass D, López-García P, Chao EE, Cavalier-Smith T ( 2007 ) Global eukaryote phylogeny: combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata. Molecular Phylogenetics and Evolution 44 : 255-266 . doi:10.1016/j.ympev.2006.11.001
2006
  • Karpov SA, Bass D, Mylnikov AP, Cavalier-Smith T. ( 2006 ) Molecular phylogeny of Cercomonadidae and kinetid patterns of Cercomonas and Eocercomonas gen. nov. (Cercomonadida, Cercozoa). Protist 157 : 125-158 . doi:10.1016/j.protis.2006.01.001
2005
  • Bass D ( 2005 ) Evolution and Biodiversity of the Novel Protozoan Phylum Cercozoa., In: DPhil thesis . University of Oxford .
  • Bass D, Moreira D, López-García P, Polet S, Chao E-E, von der Heyden S, Pawlowski J, Cavalier-Smith T (2005) ( 2005 ) Polyubiquitin insertions and the phylogeny of Cercozoa and Rhizaria. Protist 156 : 149-161 . doi:10.1016/j.mib.2005.02.003
  • Richards TA, Bass D (2005) ( 2005 ) Molecular screening of free-living microbial eukaryotes: diversity and distribution using a meta-analysis. Current Opinions in Microbiology 8 : 240-252 . doi:10.1016/j.mib.2013.06.004
2004
  • Bass D, Cavalier-Smith T ( 2004 )  Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa).   International Journal of Systematics and Evolutionary Microbiology 54 : 2393-2404 . doi:10.1099/ijs.0.63229-0