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MOLECULAR ECOLOGY of MARINE ALGAL VIRUSES by JOAQUIN

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MOLECULAR ECOLOGY of MARINE ALGAL VIRUSES by JOAQUIN University of Plymouth PEARL https://pearl.plymouth.ac.uk 04 University of Plymouth Research Theses 01 Research Theses Main Collection 2006 MOLECULAR ECOLOGY OF MARINE ALGAL VIRUSES MARTINEZ, JOAQUIN MARTINEZ http://hdl.handle.net/10026.1/2459 University of Plymouth All content in PEARL is protected by copyright law. Author manuscripts are made available in accordance with publisher policies. Please cite only the published version using the details provided on the item record or document. In the absence of an open licence (e.g. Creative Commons), permissions for further reuse of content should be sought from the publisher or author. MOLECULAR ECOLOGY OF MARINE ALGAL VIRUSES By JOAQUIN MARTINEZ MARTINEZ A thesis submitted to the University of Plymouth for the degree of DOCTOR OF PHILOSOPHY Department of Biological Sciences University of Plymouth In collaboration with The Marine Biological Association (UK) Plymouth Marine Laboratory (UK) University of Bergen (Norway) September 2006 ~~ University ofiPiymol!th · 1 ~ ll.ibrary; I . -- ~ · ~ltem,No 'C?!oO:I),'lC,SI Of+ _ ~.,l. Shelfmark . .. i T~E.'OIS SliJ' .. ~(Q£\.~. b$-. tl~ . - . • , I This copy of,therthesis hlis. been !;llpplied of\:cohditicmthat anyone who:consults it is :understood I to recognise thahts;.copyright rests with its author 1111<1 ,tllM r\6 quotation' from the thesi.sian<i i1o ifl[orniation,denvedl from. it may'oe publishedi without .the'author's prior consent. b " Joaquin Martinez Martinez Molecular Ecology of Marine Algal Viruses IAbstract In this study phytoplankton viruses were investigated from a point of view of their genotypic richness, ecology and role in controlling two microalgae species: Emiliania huxleyi and Phaeocystis pouchetii. Host specificity determined for Emiliania huxleyi-virus (Eh V) isolates revealed a highly variable host range suggesting a relation between virus specificity and genetic or phenotypic variations within E. huxleyi strains and Eh Vs. Subsequently the dynamics and genetic richness of Emiliania huxleyi and Eh Vs were monitored in mesocosm experiments and during the progression of a natural bloom in the sea. The results confirmed the role of virus infection in regulating the intraspecific succession of E. huxleyi in the ocean. Furthermore, they revealed significant differences in genotypic composition and dynamics among blooms. The mesocosm setup appeared to be a very robust experimental system, which allowed reproducibility. The most important factor determining the development of the blooms in the enclosures was the experimental manipulation (i.e. nutrient addition), whereas the effect of filling of the enclosures, delay in nutrient addition and position in the raft were of minor importance. Further laboratory experiments revealed differences in the genomic content of different Eh Vs. Eh V isolates from the English Channel carry a putative phosphate permease gene ( ehv I 17) while the only available Eh V from a Norwegian fjord has replaced ehv 11 7 with a putative endonuclease, suggesting different propagation strategies among closely related Eh Vs. Culture studies using one of the English Channel isolates and E. huxleyi CCMP 1516 showed that the lack of phosphate (P) reduced the growth rate of the host and inhibited the production of viral particles. Furthermore, P availability was shown to have an effect on the level of ehv 117 expression. In addition, other mesocosm studies revealed that specific viruses (Pp Vs) play a significant role in the termination of induced Phaeoc:vstis pouchetii blooms. However, the role of Pp Vs may be significant only for the flagellated stage of P. pouchetii. Phenotypic characteristics ofPpVs isolated during these studies indicate that they are probably members of the Phycodnaviridae family. 11 I List of contents Page I. Introduction .......................................................................................... I 1.1. Oceanic biogeochemistry ...................................................................... I 1.2. Phytoplankton dynamics ....................................................................... 2 1.3. Detection and discrimination ofphytoplankton groups ...................................... 5 1.4. Phytoplankton species subject of study in the thesis ...................................... 5 1.4.1. Emiliania huxleyi ........................................................................ 6 1.4.2. Phaeocystis pouchetii .................................................................. 8 1.5. The origins of marine virology ................................................................. 9 I .6. Algal viruses .................................................................................... I I 1.7. Role ofphytoplankton viruses ................................................................ 19 1.7.1. Viral-mediated mortality: impact on abundance, structure and community dynamics ....................................................................................... 19 I. 7 .2. Biogeochemical and ecological implications ...................................... 21 1.8. Factors that influence viral infection and replication .................................... 23 1.9. Host resistance to viral infection ............................................................ 24 I. I 0. Viral decay ................................................................................... 27 1.11. Aims of the project .......................................................................... 28 2. Material and methods .............................................................................. 30 2.1. Materials ....................................................................................... 30 2.1.1. Chemicals, reagents and laboratory consumables ................................ 30 2.1.2. Commonly used solutions ........................................................... 30 2.1.3. Growth media ......................................................................... 31 2.1.4. Virus isolates .......................................................................... 31 2.1.5. Phytoplankton strains ................................................................ 32 2.1.6. Oligonucleotides ..................................................................... 35 2.2. General methods ............................................................................... 36 Ill 2.2.1. Concentration and storage of sea water samples and vira11ysates .............. 36 2.2.2. Maintenance ofphytoplankton cultures ........................................... 36 2.2.3. Isolation of new viruses .............................................................. 36 2.2.3.1. Inoculation ofphytoplankton-host cultures .................................. 36 2.2.3.2. Enrichment cultures ............................................................. 37 2.2.3.3. Plaque assay ..................................................................... 37 2.2.4. Host range determination ............................................................ 38 2.2.5. Cell photosynthetic capacity (CPC) ................................................ 38 2.2.6. Analytical flow cytometry (AFC) .................................................. 39 2.2.7. Enumeration ofphytoplankton cells and colonies by light microscopy ...... 40 2.2.8. Transmission Electron Microscopy (TEM) ...................................... .40 2.2.9. Dialysis of virus lysates for removal of excess nutrients ........................41 2.2.1 0. Pulse field gel electrophoresis (PFGE) ......................................... .41 2.2.11. Nucleic acid isolation and quantification ...................................... .42 2.2.11.1. Hexadecyltrimethyl ammonium bromide (CT AB) method for DNA extraction from virus lysates ............................................................ .42 2.2.11.2. Phenol/chloroform DNA extraction .........................................43 2.2.11.3. Isolation of total RNA from infected and uninfected cells .............. .44 2.2.11.4. DNase treatment of RNA samples ......................................... .45 2.2.11.5. Nucleic acid quantification .................................................. .45 2.2.12. Amplification of DNA fragments by polymerase chain reaction (PCR) .... 45 2.2.13. Agarose gel electrophoresis ....................................................... .46 2.2.14. Denaturing gradient gel electrophoresis (DOGE) ............................. .46 2.2.15. Automated DNA sequencing ..................................................... .47 2.2.16. Molecular cloning .................................................................. .48 2.2.17. Isolation ofrecombinant plasmid DNA ......................................... .48 2.2.18. Reverse-transcription reactions .................................................. .48 IV 2.2.18.1. Production of RNA transcripts from DNA fragments .................... .48 2.2.18.2. Synthesis of cDNA from total RNA ........................................ .49 2.2.19. Real-time PCR ........................................................................ 49 2.2.19.1. Detection of fluorescence contaminants ................................... .49 2.2.19.2. Primers and probe design and optimisation ................................ 50 2.2.19.3. PCR reaction mix .............................................................. 50 2.2.19.4. Construction of calibration curve ............................................ 50 2.2.20. Mesocosm experiments ............................................................ 51
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