Microbial life defines most of the biogeochemical properties of our oceans. The interactions that take place between marine biogeochemical cycles and marine microorganisms are profound.

"The role of the infinitely small in Nature is infinitely great" - Louis Pasteur

Microorganisms are the most abundant components of marine ecosystems, and have a diverse array of metabolic functions that control biogeochemical cycles and maintain the earth system. Connecting microbial phylogenetic diversity and metabolic capability with biogeochemical processes is vital to achieve a comprehensive understanding of marine ecosystem structure and functioning

The Cunliffe Research Group at the MBA is focused on understanding the underpinning mechanisms, both ecological and physiological, by which microorganisms sustain marine biogeochemical cycles and other ecosystem services. The multidisciplinary research integrates contemporary omics approaches with analytical biogeochemical techniques and classic microbiological methods, combining field-based observation of complex microbial assemblages and laboratory-based experiments using model microorganisms.

Below are examples of current and recent research projects that illustrate the approach of the Cunliffe Group, combining both field-based and laboratory-based microbial biology and ecology.......

Carbon monoxide oxidation in the abundant Marine Roseobacter Clade (MRC). Annotation of multiple MRC genomes has revealed that an abundance of carbon monoxide dehydrogenase cox genes are present, implying a role for the MRC in marine CO cycling. I have established the link between cox genes and metabolic function (i.e. CO oxidation). cox genes fall into two different forms; form I and form II. Only MRC strains with form I cox genes can oxidise CO (Cunliffe 2011). Even though Ruegeria pomeroyi expresses CO dehydrogenase and oxidises CO, CO has no effect on growth or cellular metabolite profiles (Cunliffe 2013). These results are important because they validate ecosystem models that propose, even though bacterioplankton CO oxidation is biogeochemically significant, it has an insignificant effect on bacterioplankton productivity.

Purine degradation and nitrogen regeneration in Ruegeria pomeroyi. Using transcriptomics (RNASeq, Illumia Hiseq), I have established the metabolic pathways active in R. pomeroyi during xanthine degradation. This is the first study to characterise purine utilisation in a marine bacterium. The transcriptome-deduced pathway indicates that ammonia is produced during xanthine catabolism (Cunliffe 2016). Ammonia is an important source of regenerated nitrogen that sustains phytoplankton productivity throughout the summer once nitrate has been depleted (Ward et al 2011).

Polychaete burrows harbour distinct microbial communities in oil-contaminated coastal sediments and enhance bioremediation. Bioturbation of oil-contaminated sediments by the model burrowing infauna organism Hediste (Nereis) diversicolor accelerates hydrocarbon breakdown and causes significant changes in bacterial community composition, including the enhancement of aerobic hydrocarbon-degrading bacteria. Infauna also change eukaryote community composition, including the stimulation of bacterivorous protists and nematodes (Taylor and Cunliffe 2015).

Ocean acidification influences microbial biofilm diversity. We compared biofilms that colonised glass slides along a natural coastal CO2/pH gradient. Biofilm production was enhanced when grown at high CO2, and showed clear differences in community structure (Lidbury et al 2012). More recently, we examined intertidal epilithic biofilms at the same locations using high-throughput sequencing and showed that under high CO2/low pH seawater conditions, biofilm diversity is significantly alerted (Taylor et al 2014). These studies provide baseline understanding of how coastal ecosystems may respond to increased CO2 levels (Brodie et al 2014).

References

Brodie J, Williamson CJ, Smale DA, Kamenos NA, Mieszkowska N, Santos R et al (2014). The future of the northeast Atlantic benthic flora in a high CO2 world. Ecology and Evolution 4: 2787-2798.

Cunliffe M (2011). Correlating carbon monoxide oxidation with cox genes in the abundant Marine Roseobacter Clade. The ISME Journal 5: 685-691.

Cunliffe M (2013). Physiological and metabolic effects of carbon monoxide oxidation in the model marine bacterioplankton Ruegeria pomeroyi DSS-3. Applied and Environmental Microbiology 79: 738-740.

Cunliffe M (2016). Purine catabolic pathway revealed by transcriptomics in the model marine bacterium Ruegeria pomeroyi DSS-3. FEMS Microbiology Ecology 92 DOI: 10.1093/femsec/fiv1150

Lidbury I, Johnson V, Hall-Spencer J, Munn C, Cunliffe M (2012). Community-level response of coastal microbial biofilms to ocean acidification in a natural carbon dioxide vent ecosystem. Marine Pollution Bulletin 64: 1063-1066.

Taylor JD, Ellis R, Milazzo M, Hall-Spencer JM, Cunliffe M (2014). Intertidal epilithic bacteria diversity changes along a naturally occurring carbon dioxide and pH gradient. FEMS Microbiology Ecology 89: 670-678.

Taylor JD, Cunliffe M (2015). Polychaete burrows harbour distinct microbial communities in oil-contaminated coastal sediments. Environmental Microbiology Reports 7: 606-613.

Ward BB, Rees AP, Somerfield PJ, Joint I (2011). Linking phytoplankton community composition to seasonal changes in f-ratio. The ISME Journal 5: 1759-1770.

MARINe-DNA: Development and application of eDNA tools to assess the structure and function of coastal sea ecosystems

The MARINe-DNA project will test the overarching hypothesis that marine-derived environmental DNA (eDNA) is a biodiversity proxy that can be used to inform our understanding of marine biodiversity and ecosystem structure/function relationships. The project will be split into three phases that...

Integrated Biotechnological Solutions for Combating Marine Oil Spills (Kill Spill)

Oil spills that release harmful petroleum hydrocarbons into the marine environment can be cleaned up in several ways. These include sponge-like sorbents that absorb oil, dispersants that chemically break down oil, and microorganisms that biologically degrade oil by consuming it as an energy...

Staff List

Michael Cunliffe
MBA Research Fellow
Since 2014 Lecturer (Joint Appointment with MBA) Marine Institute, Plymouth University Since 2014 Honorary Lecturer School of Environmental Sciences, University of East Anglia Since 2010 MBA Research Fellow (Principal Investigator) Marine Biological Asso
Email: Telephone Number:
+44(0)1752 426328
Kimberley Bird
PhD student
Kim is currently carrying out research at the Marine Biological Association UK for her PhD, entitled: The marine microbial biogeochemistry of carbon monoxide – connecting biodiversity with ecosystem function.
Email: Telephone Number:
+44(0)1752 968707
Harriet Dale
PhD Student
Harriet is a PhD student studying the effect of invertebrate bioturbation on sediment microbial communities, with a particular interest in microbes that mediate nitrogen cycling processes.
Email: Telephone Number:
+44(0)1752 426257

25. Taylor JD & Cunliffe M (2017) Coastal bacterioplankton community response to diatom-derived polysaccharide microgels. Environmental Microbiology Reports in press

24. Taylor JD & Cunliffe M (2016) Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance. The ISME Journal 10: 2118-2128

23. Cunliffe M (2016) Purine catabolic pathway revealed by transcriptomics in the model marine bacterium Ruegeria pomeroyi DSS-3. FEMS Microbiology Ecology in press

22. Taylor JD & Cunliffe M (2015) Polychaete burrows harbour distinct microbial communities in oil-contaminated coastal sediments. Environmental Microbiology Reports 7: 606–613.

21. Taylor JD, Ellis R, Milazzo M, Hall-Spencer JM & Cunliffe M (2015) Intertidal epilithic bacteria diversity changes along a naturally occurring carbon dioxide and pH gradient. FEMS Microbiology Ecology 89:670-8.

20. Taylor JD & Cunliffe M (2014) High-throughput sequencing reveals neustonic and planktonic protist diversity in coastal waters. Journal of Phycology 50: 960–965.

19. Brodie J,.Cunliffe M et al (2014) The future of the northeast Atlantic benthic flora in a high CO2 world. Ecology and Evolution 4: 2787–2798.

18. Taylor JD, Cottingham SD, Billinge J & Cunliffe M (2014) Seasonal microbial community dynamics correlate with phytoplankton-derived polysaccharides in surface coastal waters. The ISME Journal 8: 245–248.

17. Kadar E, Cunliffe M, et al (2014) Chemical interaction of atmospheric mineral dust-derived nanoparticles with natural seawater - EPS and sunlight-mediated changes. The Science of the Total Environment 468-469: 265-271.

16. Cunliffe M (2013) Physiological and metabolic effects of carbon monoxide oxidation in the model marine bacterioplankton Ruegeria pomeroyi DSS-3. Applied and Environmental Microbiology 79: 738-740.

15. Cunliffe M et al (2013) Sea surface microlayers: A unified physicochemical and biological perspective of the air–ocean interface. Progress in Oceanography 109: 104-116.

14. Lidbury L, Johnson V, Hall-Spencer JM, Munn CB & Cunliffe M (2012) Community-level response of coastal microbial biofilms to ocean acidification in a natural carbon dioxide vent ecosystem. Marine Pollution Bulletin 64: 1063–1066. 

13. Boden R, Cunliffe M, et al (2011) Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09. Journal of Bacteriology 193 (24): 7001-7002.

12. Cunliffe M (2011) Correlating carbon monoxide oxidation with cox genes in the abundant Marine Roseobacter Clade. The ISME Journal 5: 685-691.

11. Lobelle D & Cunliffe M (2011) Early microbial biofilm formation on marine plastic debris. Marine Pollution Bulletin 62: 197-200.

10. Cunliffe M, Upstill-Goddard RC & Murrell JC (2011) Microbiology of aquatic surface microlayers. FEMS Microbiology Reviews 35 (2): 233-246.

9. Cunliffe M & Murrell JC (2010) Eukarya 18S rRNA gene diversity in the sea surface microlayer: insights on the structure of the neustonic microbial loop. The ISME Journal 4: 455-458.

8. Cunliffe M et al (2009) Comparison of bacterioneuston and bacterioplankton dynamics during a phytoplankton bloom in a fjord mesocosm. Applied and Environmental Microbiology 75 (22): 7173-7181. 

7. Cunliffe M et al (2009) Dissolved organic carbon and bacterial populations in the gelatinous surface microlayer of a Norwegian fjord mesocosm. FEMS Microbiology Letters 299 (2): 248-254.

6. Cunliffe M & Murrell JC (2009) The sea surface microlayer is a gelatinous biofilm. The ISME Journal 3: 1001–1003.

5. Cunliffe M et al (2009) Comparison and validation of sampling strategies for the molecular microbial ecological analysis of surface microlayers. Aquatic Microbial Ecology 57: 69-77.

4. Cunliffe M et al (2008) Phylogenetic and functional gene analysis of the bacterial and archaeal communities associated with the surface microlayer of an estuary. The ISME Journal 2: 776–789.  

3. Cunliffe M et al (2006) Effect of inoculum pre-treatment on survival, activity and catabolic gene expression of Sphingobium yanoikuyae B1 in an aged polycyclic aromatic hydrocarbon-contaminated soil. FEMS Microbial Ecology 58: 364-372.

2. Cunliffe M & Kertesz MA (2006) Autecological properties of soil sphingomonads involved in the degradation of polycyclic aromatic hydrocarbons. Applied Microbiology and Biotechnology 72: 1083-1089.

1. Cunliffe M & Kertesz MA (2006) Effect of Sphingobium yanoikuyae B1 inoculation on bacterial community dynamics and polycyclic aromatic hydrocarbon degradation in aged and freshly PAH- contaminated soils. Environmental Pollution 144: 228-237.

Dr Michael Cunliffe

Marine Biological Association of the UK 

The Laboratory

Citadel Hill 

Plymouth PL1 2PB

Email: micnli@mba.ac.uk