Skip to main content

Marine microbiology

Research Leader: Professor David Scanlan

Google Scholar

A major research theme in the group is to use molecular biological techniques to assess the genotype and nutrient status of marine photosynthetic microbes so that the specific factors controlling marine photosynthesis in single cells can be identified. In addition, we are using molecular genetic tools and molecular ecological approaches to investigate the way these organisms perceive and adapt to changes in their environment, and particularly how certain strains have adapted to occupy a specific niche. Thus, we are using fine-scale genetic markers and high throughput sequencing to assess the community structure of photosynthetic microbes over large spatial scales, and coupling this with meta-‘omic approaches to decipher the functional potential and in situ activity of these organisms. We focus on both the role of abiotic (light, nutrients) and biotic (virus infection, protistan grazing) factors in controlling the abundance of these organisms. Moreover, functional identification of genes implicated as playing a specific role in the adaptation of marine (and freshwater) cyanobacteria to their environment is being pursued by mutant construction and analysis. This latter work is being greatly aided by the recent completion of various Prochlorococcus and marine Synechococcus genomes see http://abims.sb-roscoff.fr/cyanorak/. This is paving the way for detailed comparative genomic (transcriptomic and proteomic) analyses in these organisms and the viruses that infect them.

jpeg

Work focuses on the following key groups of picophotoautotrophs, organisms which are widespread and abundant in marine ecosystems, and contribute significantly to global primary production. Hence, these are environmentally relevant organisms and all contain cultured counterparts. The cyanobacterial component are also capable of growth at a wide range of irradiance and in waters with low or undetectable levels of inorganic nutrients:

  • Prochlorococcus
  • Synechococcus
  • Picoeukaryotes

Other recent research avenues in the Scanlan lab include projects on i) marine heterotrophic bacterioplankton, particularly focusing on lipid remodeling, degradation of N osmolytes, and phototroph-heterotroph interactions and ii) P acquisition mechanisms in the plant-rhizosphere.

 

Current Group Members

Dr Rich Puxty (Postdoctoral research assistant), Dr Frances Pitt (Postdoctoral research assistant), Dr Ian Lidbury (Postdoctoral Research Assistant), Dr Michaela Mausz (Postdoctoral research assistant), Alicja Dabrowska (4th year PhD student), Despoina Sousoni (3rd Year PhD student), Tamsin Redgwell (2nd year PhD student), Alevtina Mikhaylina (2nd year PhD student), Slawek Michniewski (1st Year PhD student), Betty Sands (1st Year PhD student), Rebekah Jones (1st Year PhD student), Julie Scanlan (Research technician).

People and projects

Dr. Francis Pitt, Postdoctoral researcher

Fran Pitt

Obtaining a mechanistic understanding of viral photosynthesis

Marine viruses have a critical role in global biogeochemical cycling. They are responsible for the release of 150 Gt of carbon per year from phytoplankton lysis and therefore structure oceanic microbial communities by host lysis.

Cyanophages capable of infecting cyanobacteria (responsible for 30-90% of ocean primary productivity) are exceptional in that they also appear to play a direct role in CO2 fixation since they carry genes that are essential for photosynthesis. The significance of phage mediated photosynthesis and its potential contribution to global CO2 fixation in marine environments could strongly impact biogeochemical cycling models and ocean carbon budget predictions.


The project aims to advance our knowledge by determining how cyanophage mechanistically control expression of host derived photosynthesis genes, particularly focusing on the role of non-coding RNAs

Dr. Frances Pitt brings to the project an established skill set for the genetic manipulation of both freshwater and marine cyanobacteria. Previous project outputs have demonstrated the molecular basis for regulation and control of cyanobacterial responses to changes in environmental variables. Her recent work on marine Synechococcus fine scale community structure and natural environment metagenomics/transcriptomic analysis provides an ideal springboard for the investigation into host-phage interaction and the molecular mechanisms for its photosynthetic control.

Cyanophage

Dr Rich Puxty, Postdoctoral researcher

We have recently shown that viruses of abundant marine cyanobacteria shut down CO2 fixation during infection. Rich’s project builds on this, focusing on assessing how marine Synechococcus CO2 fixation varies during cyanophage infection under a range of environmental conditions, particularly under conditions of host nutrient limitation. The project also aims to provide a mechanistic understanding of the process.

Dr Ian Lidbury, Postdoctoral Researcher

Ian’s research focuses on the mobilisation of phosphorus in the rhizosphere of Oil Seed Rape (Brassica napus).

Dr Michaela Mausz, Postdoctoral Researcher

Michaela is investigating the biogeochemical cycling of the N-containing osmolytes choline and glycine betaine.

dabrowska_a_130x180.jpgAlicja Dabrowska, PhD student

Opening up the black box of marine phototroph-heterotroph interactions.

Funded through the NERC and co-supervised by Dr. Chris Corre and Dr. Joseph Christie-Oleza, this interdisciplinary project focuses on interactions between phototrophs and heterotrophs co-existing in the open ocean. Following interactions between model Synechococcus and Roseobacter bacteria, we aim to characterize novel biomolecules, to determine pathways involved in production and potential consumption of these molecules, and to describe the prevalence of such biosynthetic pathways in marine systems.

 Despoina Sousoni photoDespoina Sousoni, PhD student

In my PhD project I am investigating interactions between key relevant marine phytoplankton (i.e. picocyanobacteria, green algae, diatoms and haptophytes) and various heterotrophic bacteria (i.e. actinobacteria, bacteroidetes, alpha- and gamma-proteobacteria, planctomycetes and verrucromicrobia), in one-to-one co-cultures focusing on i) culture physiology, ii) nutrient stoichiometry iii) cellular proteomics and iv) exometabolomics. This study brings us a step closer to understanding complex microbial networks and helps explain the evolutionary success of specific microbial groups in natural marine systems. This project is funded by the NERC CENTA DTP and supervised by Dr. Joseph Christie-Oleza and Prof. Dave Scanlan.

 Tamsin RedgwellTamsin Redgwell, PhD student

Microbial ‘parasites’ meet climate change: marine cyanobacteria as viral puppets.

Funded through the NERC CENTA DTP and co-supervised by Dr Andrew Millard, Tamsin's work aims to help understand to what extend cyanophage auxiliary metabolic genes (AMGs) affect phage-host interactions, and in doing so affect global biogeochemical cycles.

Genes involved in photosynthesis are widespread in cyanophage. Phage-derived copies of photosystem II genes are thought to maintain cellular photosynthetic activity during infection and thus maximise the production of progeny phage. Cyanobacterial hosts are known to be very important in the global carbon cycle and so any manipulation of the host by infecting phage could dramatically alter their contribution to biogeochemical cycling. My project aims to use molecular techniques to assess the role of cyanophage-encoded photosynthesis genes in infection. I am using traditional chemical mutagenesis methods combined with next generation sequencing tools, to develop a cyanophage genetic system to facilitate gene function studies and the identification of novel AMGs.

Alevtina MikhaylinaAlevtina Mikhaylina, PhD student

Funded through the Warwick Chancellors Scholarship and co-supervised by Dr Claudia Blindauer and Prof Dave Scanlan, Alevtina is elucidating the Zur regulon in marine Synechococcus investigating the utilization and function of zinc in cyanobacterial metabolism.

Sands_Photo_Jul17Betty Sands, PhD student

Funded through the NERC CENTA DTP and supervised by Dr Isabelle Carré and Prof Dave Scanlan, Betty’s project is investigating the genetics and physiological consequences of light quality responses in Ostreococcus, a eukaryotic picophytoplankton abundant in the coastal ocean. Surface and deep ecotypes of Ostreococcus are being compared and the role light quality plays in adaptation to these specific niches assessed.

jones_photo_jul17.jpgRebekah Jones, PhD student

Rebekah is investigating the role of lipid remodelling in pathogenic bacteria and the implications of this for antimicrobial resistance and host-pathogen interactions. Rebekah is supervised by Dr Yin Chen and Prof Dave Scanlan and funded by the Medical Research Council Interdisciplinary Biomedical Research doctoral training programme.

Holly ShropshireHolly Shropshire, MRes Student

Holly is a Masters by Research student supervised by Dr. Elizabeth Fullam and Professor David Scanlan investigating nutrient transport in Mycobacterium tuberculosis. Holly is using synthetic biology and a model cyanobacterium to identify specific substrates of these transporters

Stirrup_PhotoRachel Stirrup, MRes Student

Rachel is a Masters by Research student supervised by Dr Joseph Christie-Oleza and Professor David Scanlan investigating cyanophage ecology with a focus on cyanophage loss factors. Rachel is also investigating how cyanophage infection influences the host Synechococcus lipidome.

Research Facilities

Excellent cyanobacterial and eukaryotic phytoplankton culturing facilities including walk-in temperature controlled growth rooms, supported by department-run media preparation service.

In House MiSeq sequencing and real-time qPCR facilities, high-speed BD Influx flow cytometric sorting capacity, LC-MS facility for metabolite detection, state-of-the-art proteomics facility, and within lab access to molecular biology, biochemistry, analytical flow cytometry and photophysiological (PhytoPAM, light array) facilities.

Collaborators

Dr Gary Bending (University of Warwick, SLS) Phosphorus acquisition in the soil plant-rhizosphere

Dr Claudia Blindauer (University of Warwick, Chemistry) Marine cyanobacterial metalloproteomics

Dr Yin Chen (University of Warwick, SLS) Marine heterotroph phospholipid recycling and N osmolyte degradation

Dr Joseph Christie-Oleza (University of Warwick, SLS) Marine phototroph-heterotroph interactions

Dr Martha Clokie (University of Leicester, UK) Marine cyanophage

Dr Christophe Corre (University of Warwick, SLS/Chemistry) Structure and function of cyanobacterial metabolites

Dr Laurence Garczarek (Station Biologique, Roscoff, France) Prochlorococcus and Synechococcus molecular ecology and genomics

Dr Mikal Heldal (University of Bergen, Norway) Elemental composition of marine picocyanobacteria

Prof Wolfgang Hess (University of Freiburg, Germany) Marine picocyanobacteria genomics and small RNAs

Dr Wei Huang (University of Oxford) Raman spectroscopy

Dr Martin Ostrowski (Macquarie University, Sydney) Synechococcus metagenomics/biodiversity

Dr Frederic Partensky (Station Biologique, Roscoff, France) Prochlorococcus and Synechococcus molecular ecology and genomics

Prof Anton Post (Florida Atlantic University, USA) Prochlorococcus and Synechococcus molecular ecology and genomics

Dr Christophe Six (Station Biologique, Roscoff, France) Marine cyanobacterial lipids

Prof Paul Taylor University of Leeds - The Evolutionary Origins of Chemical Messengers in Humans

Dr Osvaldo Ulloa (Universidad de Concepción, Chile) Prochlorococcus and Synechococcus community structure in oxygen minimum zones

Dr Daniel Vaulot (Station Biologique, Roscoff, France) Picoeukaryote biodiversity and genomics

Prof Liz Wellington (University of Warwick, SLS) Metaproteomics of phosphorus acquisition in the soil plant-rhizosphere

Dr Mike Zubkov (National Oceanography Centre, Southampton) Flow sorting of cyanobacteria and photosynthetic picoeukaryotes/Mixotrophy/Grazing

 

Prospective Students and postdoctoral researchers

Students interested in pursuing graduate research with Prof. Scanlan are encouraged to contact him directly by email (d.j.scanlan@warwick.ac.uk). For more information about graduate programs at the University of Warwick see http://www2.warwick.ac.uk/fac/sci/lifesci/study/pgr/research/phd

Prospective postdoctoral researchers with interests in the field of marine microbiology, particularly photosynthetic microorganisms are encouraged to contact Prof. Scanlan directly by email (address above) to discuss potential research projects and funding opportunities.