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Microbiology Logo Microbiology & Immunology
Te Tari Moromoroiti me te Ārai Mate

Dr Simon Jackson

Current research:

The overall aim of my research group is to understand the interactions between bacterial viruses (phages) and their hosts. Currently, we are funded to study bacterial phage defence systems, such as CRISPR-Cas adaptive immune systems. With the rise of antimicrobial resistance (AMR) in bacterial pathogens, we urgently need to find new ways to treat bacterial infections. Exploiting phages as natural antimicrobials to kill bacterial pathogens, termed phage therapy, is a promising approach to address the AMR crisis. However, the success of phage therapy is dependent on understanding the complex interaction between phages and bacteria. To address these challenges, we use a combination of bioinformatic, comparative genomics and molecular biology approaches. In 2017, I was awarded the IlluminaTM Emerging Researcher Award, as the top New Zealand Molecular Biologist within 5 years of PhD completion.

Areas of Current Research Focus:

  • Understanding how bacteria update their CRISPR-Cas adaptive immune systems, termed CRISPR adaptation.
  • Exploring cooperation between diverse CRISPR-Cas systems to prevent viral escape from immunity.
  • Discovery and characterisation of new types of phage defense system encoded by bacteria.
  • The relationships between phage defense and symbiosis in Rhizobia.


  • Exploiting phages to enhance legume productivity.
  • Developing new types of molecular diagnostics to detect bacterial and viral infections.
  • Exploiting phage-encoded enzymes as new antimicrobials.


Google Scholar:



Maurice Wilkins Center for Molecular Biodiscovery

Postgraduate Student (co)-supervision:


Leighton Payne, current

Nils Birkholz, current

Leah Smith, 2016-2020

Hannah Hampton, 2015-2018


Stephanie Trickey, current

Bridget Fellows, 2020

Nils Birkholz, 2016

Julian Taffner, 2014


Thomas Hughes, 2021

Thomas Ware, 2020

Leighton Payne, 2019

Maureen Yin, 2019

Nick Donaldson, 2018

Matthew Prouse, 2014

Lauren Nichol, 2014

Jack Hervey, 2013

Summer studentships:

Aileen Harwood, 2020-2021

Leighton Payne, 2019-2020

Maureen Yin, 2018-2019

Nick Donaldson, 2017-2018

Jack Hervey, 2012-2013


Research Funding and Fellowships:

2020   Deans Bequest ($12,500) as PI. ‘The relationship between nitrogen fixation and bacteriophage resistance in Rhizobium leguminosarum.’

2020   Marsden Grant (RSNZ, $960,000) as AI (PI: Prof. Peter Fineran). ‘How do bacterial CRISPR-Cas defences protect against nucleus-forming phages?’

2020   Health Research Council Project ($1,199,272) as AI (PI: Dr Matthew McNeil). ‘Combating antimicrobial resistance with high throughput bacterial genetics.’

2019   University of Otago Research Grant ($37,471) as PI. ‘A new approach to discover phage defence systems in bacteria.’

2019   MBIE SmartIdeas ($1,000,000) as a Key Researcher (PI: Prof. Peter Fineran). ‘Phage-inspired custom antimicrobials to target bacterial pathogens.’

2019   Deans Bequest (University of Otago, $21,000) as PI. ‘New types of phage defences encoded in bacterial genomes.’

2019   Maurice Wilkins Centre Flexible Research Grant ($26,000) as an AI (PI: Dr Jeremy Owen, Victoria University of Wellington). ‘Development of new synthetic biological tools for cloning and expression of antibiotic biosynthetic gene clusters from microbial genomes.’

2018   Marsden Fast Start Grant (RSNZ), as PI ($300,000) (AI: Prof. Antonio Sánchez-Amat, University of Murcia, Spain). ‘Mobile CRISPR-Cas systems and the genesis of hybrid adaptive immunity in bacteria.’

2018   EMBO Workshop ‘Viruses of Microbes 2018’ travel grant (€500).

2017   Deans Bequest (University of Otago, $16,000) as an AI (PI: Prof. Peter Fineran). ‘Chimeric CRISPR-Cas systems – the evolution of new bacterial immunity?’

2016   Deans Bequest (University of Otago, $21,648) as an AI (PI: Prof. Peter Fineran). ‘You’re 1 in a million: a novel high-throughput methodology for finding key regulators of gene expression in bacteria.’

2013   Division of Health Sciences Career Development Postdoctoral Fellowship (~$150,000, University of Otago). ‘Assembly and photoprotection of Photosystem II in Synechocystis sp. PCC 6803.’


* Equal contribution authors; # Corresponding author


Smith, L.M., Jackson, S.A., Malone, L.M., Ussher, J.E., Gardner, P.P. and Fineran, P.C.# (2020) The Rcs stress response inversely controls surface and CRISPR-Cas adaptive immunity to discriminate plasmids and phages. Nature Microbiology, 6: 162-172

Hampton, H.G., Smith, L.M., Ferguson, S., Meaden, S., Jackson, S.A. and Fineran, P.C.# (2020) Functional genomics reveals the toxin-antitoxin repertoire and AbiE activity in Serratia. Microbial Genomics, 6: 1-15

Jackson, S.A.#, Fellows, B.J. and Fineran, P.C. (2020) Complete genomes of the Escherichia coli donor strains ST18 and MFDpir. Microbiology Resource Announcements, 9: e01014-20

Malone, L.M., Warring, S.L., Jackson, S.A., Warnecke, C., Gardner, P.P., Gumy, L.F. and Fineran, P.C.# (2020) A jumbophage that forms a nucleus-like structure evades CRISPR–Cas DNA targeting but is vulnerable to type III RNA-based immunity. Nature Microbiology, 5: 48-55


Jackson, S.A. and Fineran, P.C. (2019) Bacterial dormancy curbs phage epidemics. Nature, 570: 173-174.

Birkholz, N., Fagerlund, R.D.*, Smith, L.M., Jackson, S.A.* and Fineran, P.C.# (2019) The autoregulator Aca2 mediates anti-CRISPR repression. Nucleic Acids Research, 47: 9658-9665

Jackson, S.A.#, Birkholz, N., Malone, L.M. and Fineran, P.C.# (2019) Imprecise spacer acquisition generates CRISPR-Cas immune diversity through primed adaptation. Cell Host and Microbe, 25: 250-260

Nicholson, T.J.*, Jackson, S.A.*, Croft, B.I., Staals, R.H.J., Fineran, P.C.# and Brown, C.M. # (2019) Bioinformatic evidence of widespread priming in Type I and II CRISPR-Cas systems. RNA Biology, 16: 566-576


Hampton, H.G., Jackson, S.A., Fagerlund, R.D., Vogel, A.I.M., Dy, R.L., Blower, T.R. and Fineran, P.C. # (2018) AbiEi Binds Cooperatively to the Type IV abiE Toxin-Antitoxin Operator Via a Positively-Charged Surface and Causes DNA Bending and Negative Autoregulation. Journal of Molecular Biology, 430: 1141-1156


Silas, S., Lucas-Elío, P., Jackson, S.A., Aroca-Crevillén, A., Hansen, L.L., Fineran, P.C., Fire, A.Z. and Sánchez-Amat, A.# (2017) Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems. eLife, 6. e27601

Jackson, S.A.*, McKenzie, R.E.*, Fagerlund, R.D., Kieper, S.N., Fineran, P.C.# and Brouns, S.J.J.# (2017) CRISPR-Cas: adapting to change. Science, 356: eaal5056. doi: 10.1126/science.aal5056


Patterson, A.G., Jackson, S.A., Taylor, C., Evans, G.B., Salmond, G.P., Przybilski, R., Staals, R.H.J. and Fineran, P.C.# (2016) Quorum sensing controls adaptive immunity through multiple CRISPR-Cas systems. Molecular Cell, 64: 1102-1108

Staals, R.H.J., Jackson, S.A., Biswas, A., Brouns, S.J.J., Brown, C.M. and Fineran, P.C.# (2016) Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR-Cas system. Nature Communications, 7: 12853

Jackson, S.A. and Eaton-Rye, J.J.# (2016) Modular growth vessels for the cultivation of the cyanobacterium Synechococcus sp. PCC 7002. New Zealand Journal of Botany, DOI: 10.1080/0028825X.2016.1231123


Jackson, S.A.*, Eaton-Rye, J.J., Bryant, D.A. Posewitz, M.C. and Davies, F.K.*,# (2015) Dynamics of photosynthesis in a glycogen-deficient glgC mutant of Synechococcus sp. PCC 7002. Applied and Environmental Microbiology, 81: 6210-6222

Jackson, S.A. and Eaton-Rye, J.J.# (2015) Characterization of a Synechocystis sp. PCC 6803 double mutant lacking the CyanoP and Ycf48 proteins of Photosystem II. Photosynthesis Research, 124: 217-229


Jackson, S.A., Hervey, J.R.D., Dale, A.J. and Eaton-Rye, J.J.# (2014) Removal of both Ycf48 and Psb27 in Synechocystis sp. PCC 6803 disrupts Photosystem II assembly and alters QA- oxidation in the mature complex. FEBS Letters, 588: 3751-3760

Luo, H., Jackson, S.A., Fagerlund, R.D., Summerfield, T.C. and Eaton-Rye, J.J.# (2014) The importance of the hydrophilic region of PsbL for the plastoquinone electron acceptor complex of Photosystem II. Biochim Biophys Acta Bioenergetics, 1837: 1435-1446


Jackson, S.A., Fagerlund, R.D., Hinds, M.G., Wilbanks, S.M. and Eaton-Rye, J.J. (2013) Structure-function studies of the Photosystem II extrinsic subunits PsbQ and PsbP from the cyanobacterium Synechocystis sp. PCC 6803. Photosynthesis for Food, Fuel and the Future. Springer, 86-90.


Jackson, S.A., Hinds, M.G. and Eaton-Rye, J.J.# (2012) Solution structure of CyanoP from Synechocystis sp. PCC 6803: New insights on the structural basis for functional specialization amongst PsbP family proteins. Biochim Biophys Acta Bioenergetics, 1817: 1331-1338


Jackson S.A.*, Fagerlund R.D.*, Wilbanks S.M. and Eaton-Rye J.J.# (2010) Crystal structure of PsbQ from Synechocystis sp. PCC 6803 at 1.8 Å: implications for binding and function in cyanobacterial Photosystem II. Biochemistry, 49: 2765-2767