virus projects funded by m&fmb

1. Influence of viruses on biogeochemical cycling

2. Bacteriophage biodiversity and horizontal gene transfer in the marine environment

3. Determining the exploitation potential of novel algal virus enzymes

4. Lambda integrase gene family: markers for phage diversity, environmental regulation and gene transfer in freshwater bacteria

5. Viruses and phytoplankton blooms: a modelling system

6. Virus dynamics in aquatic systems – an insight into the differences between marine and freshwater environments

Influence of viruses on biogeochemical cycling
Research team:	Willie Wilson (MBA/PML) Gill Malin (Univ East Anglia) Declan Schroeder (MBA) Michael Steinke (Univ East Anglia) Claire Evans (Univ East Anglia/PML) Joanne Oke (MBA)	whw@mba.ac.uk
£198.4k, 3yr from Jan 2001; 1 PDRA and research studentship Viral lysis plays a key role in natural marine ecosystems by affecting microbial biodiversity and providing a pathway for release of cell contents which are then recycled as nutrients. Hence viruses also influence global biogeochemical cycles including the production of significant trace gases. This project focuses on newly-isolated Emiliani huxleyi viruses. Following characterisation, molecular probes will be developed and used to investigate how viral lysis affects community dynamics. We shall also study viral lysis in the context of production of the volatile gas dimethyl sulphide (DMS), comparing this pathway with production via autolysis and grazing, and the involvement of algal DMSP lyase in these processes.

Bacteriophage biodiversity and horizontal gene transfer in the marine environment
Research team:	Nick Mann (Warwick) Willie Wilson (MBA/PML) Martha Clokie (Warwick)	n.h.mann@warwick.ac.uk
£185.2k; 3 yr from October 2000; PDRA The proposed research addresses the topic of bacteriophage-mediated horizontal gene transfer in the marine environment and examines the idea of a 'universal phage gene pool'. The phage infecting picophytoplanktonic marine cyanobacteria are selected as the primary group for study, and the genes encoding the phage adhesins which define the specificity of host binding have been chosen as the most appropriate locus at which to detect evidence of horizontal gene transfer. Transfer of adhesin gene segments between phages infecting the autotrophic and heterotrophic bacterioplankton and the phage-mediated transfer of plasmid and host chromosomal DNA will also be examined.

Determining the exploitation potential of novel algal virus enzymes
Research team:	Willie Wilson (MBA/PML) Declan Schroeder (MBA) Susan Wharam (PML)	whw@pml.ac.uk
£30.7k; 12 mos. from April 2004. Viruses are the most abundant biological agents in aquatic environments and possibly represent the largest unexploited biotechnological resource on the planet. Algal viruses have a long evolutionary history; consequently, algal virus specified biochemical pathways and processes might represent extremely efficient ancestral systems. There is huge exploitation potential in screening of such systems. We have sequenced the genome of an algal virus (EhV86) that infects the globally important coccolithophorid Emiliania huxleyi and we have discovered several exploitable enzyme and protein homologues. We will express, purify and screen a range of these enzymes/proteins to assess their potential for further exploitation.

Lambda integrase gene family: markers for phage diversity, environmental regulation and gene transfer in freshwater bacteria
Research team:	Jonathan Saunders (Liverpool) Roger Pickup (CEH Windermere/Lancaster) Claire Balding (Liverpool)	jrs@liv.ac.uk
£193.6k, 3 years from July 2001, 1 PDRA The primary objective is to utilise the lambda DNA integrase family as a marker for defining the distribution and diversity of mobile genetic elements, primarily temperate (lysogenic) phages, in a population of freshwater bacteria. Studies on virus interaction with bacterial populations have tended to concentrate on lytic phages and their effects on population dynamics. However, temperate phages, where lethal gene functions are repressed, may integrate into and remodel bacterial genomes and can transmit non-viral genes by transduction or phage conversion phenomena. They play an equivalent, if not greater role in the evolution and adaptation of bacterial populations: this will be the focus of the project. DNA integrases are proteins that recombine double-stranded DNA through consecutive strand breakage and rejoining. They are crucial for genome maintenance and plasticity, allowing rapid responses to environmental change, notably where they promote genome rearrangements or genetic switching. Phage lambda Int protein is the prototype DNA integrase of this family. Others maintain plasmid copy number and eliminate chromosome dimers, modulate surface components in response to environmental conditions, or are involved in the integration and excision of conjugative transposons and genomic islands. Sub-families with identifiable functions and/or sequence motifs can be identified in both Gram-positive and -negative bacteria and used potentially as markers for monitoring transfer and evolution of mobile genetic elements. We will ask the following questions: can Int genes be used to monitor the activity and diversity lysogenic phages in freshwater?; what is the extent and role of temperate phages in this environment?; what is the relationship between such phages and other genetic elements? Priest Pot will be used as the experimental site, since it is a relatively enclosed environment and we already have extensive data, stored cultures and DNA samples from this body of water.

Viruses and phytoplankton blooms: a modelling system
Research team:	Sandy Murray (Aberdeen/FRS Aberdeen)	murrays@marlab.ac.uk
£4.0k, 9 months from Feb 2001; small project contract This modelling project addresses the interaction of viruses with phytoplankton blooms, comparing lytic and lysogenic infection strategies. Under lytic infection, the virus reproduces rapidly in the host cell, causing it to burst and release large numbers of new viruses; under lysogenic infection, the host cell survives and passes on copies of the virus to daughter cells. When a large fraction of the hosts are already infected, lysogeny is expected to produce better reproductive returns. These effects will be examined in a model of viral transmission that includes effects of super-infection and environmental variation. The model has potential application to both marine and freshwater conditions, also laboratory studies of bacteriophage infections.

Virus dynamics in aquatic systems – an insight into the differences between marine and freshwater environments
Research team:	Willie Wilson (MBA/PML) David Adams (Leeds) Vicky Goddard (MBA) Andrea Baker (Leeds/MBA)	whw@pml.ac.uk
229.0k, 3 years from October 2001, 1 PDRA, 1 research studentship We propose to undertake the first detailed study on how viruses structure planktonic communities in freshwater systems using a range of molecular tools. The virus and host communities will be characterised by PFGE and DGGE over an annual cycle in three trophically different lakes in the SW of England and through depth profiles at Priest Pot. A bacterial artificial chromosome (BAC) virus genomic library will be generated from a natural virus community to characterise unculturable viruses and assess virus horizontal gene transfer processes. Specific probes will be designed to detect cyanophages and subsequently used to monitor cyanophage dynamics. Results will be compared with data obtained in similar marine projects already being conducted by WHW. The overall aim will be to assess the differences, and similarities in the role of viruses between freshwater and marine environments.