Dr Jozef I Nissimov

Microbial Oceanographer

An environmental microbiologist and biological oceanographer, researching algal-virus interactions in the context of ocean biogeochemistry, and marine virus ecology and evolution, using laboratory and field-based approaches (e.g. flow cytometry, FlowCam imaging, molecular and genomic methods, etc.)

Contact details:

My research focuses on the interactions between marine viruses and their interplay with microalgal host organisms, which are important to global biogeochemical cycles and the climate. My work spans multiple scales of biological organization, ranging from the effects of genomic and functional variability of viruses on infectivity, the physiological response of host cells to infection, the effect of environmental factors (e.g. nutrient availability) on host susceptibility to infection and virus production, and the extent to which virus-infection influences host ecology and, by extension, the fate of cell-associated organic and inorganic matter in the ocean. Other research interests include the study of microbe-microbe interactions in corals and the evolutionary relationships of algal viruses, their hosts and other taxa on the tree of life.

The tools I use in my work include a combination of molecular biology and physiological approaches to collect data on host-microbe interactions in the laboratory and the natural environment (e.g. quantitative PCR, community fingerprinting, sequencing, photophysiology and respiration, enzyme activity assays, electron microscopy, analytical flow cytometry, and FlowCam imaging). I also have a diverse fieldwork experience, which includes my participation in time-series experiments (incubations), oceanographic cruises, and large-scale mesocosm experiments.

My current goals are to address questions related to: 1) the “costs” and mechanisms of resistance to virus infection in marine microalgae; 2) the factors that affect ‘virus decay’ and inactivation; 3) the evolutionary tempo of large, dsDNA-containing viruses; 4) the biotic and abiotic stressors that drive the formation of “marine snow”, its aggregation, and ultimate sinking; and 5) the development of several novel aquatic host-virus model systems.

 

Past projects

Collaborative Research: Elucidating algal host-virus dynamics in different nutrient regimes - mechanistic interactions and biogeochemical impact

Funded by the National Science Foundation (USA), 2015-18. 

This collaborative project aimed to bridge existing gaps in the mechanistic and quantitative understanding of viruses as agents of phytoplankton mortality and their impact on biogeochemical processes.

Using lab-based experiments with a coccolithophore host-virus model system, as well as extensive datasets from virus-infected natural coccolithophore blooms in the North Atlantic, this project aimed to elucidate the impact of nutrient-limitation and host cell fitness on virus infection, and to what degree the dependence of viral infection on nutrient supply impacts large scale biogeochemistry and biogeography of a globally significant phytoplankton species.

The interdisciplinary approach combined molecular- and flow cytometry-based diagnostic techniques, with the development of mathematical models of infection, to understand the primary mechanisms underlying observed host-virus dynamics.


Examining the molecular biology and biochemistry of the lipid-based molecular arms-race regulating interactions between the coccolithophore Emiliania huxleyi and its Coccolithovirus.

Rutgers University / Gordon and Betty Moore Foundation (USA), 2013-15

A key aspect of this project was to elucidate if the competitive ecology of coccolithophore-infecting viruses is shaped at the level of a key functional gene—serine palmitoyltransferase (SPT), a rate-limiting enzyme that regulates lipid-based arms race and successful infection.

As part of this work, the structural and catalytic biochemical differences in several coccolithovirus-encoded SPTs was characterized, and it was shown that virus-derived glycosphingolipid ‘virulence factors’ exert a fundamental control on coccolithovirus infection, and that their rate of production during infection can dictate the competitive interactions between different viruses over the host machinery for infection and replication.

Through targeted next-generation sequencing of natural populations and mathematical modelling, this work was also the first to link structural enzyme biochemistry with competitive ecology of coccolithoviruses. 

In addition, the work provided foundational knowledge for how coccolithoviruses operate and interface with their algal hosts in natural environments, which are characterized by a higher diversity of different host and virus genotypes.

Peer-reviewed publications

Nissimov JI, Talmy D, Haramaty L, Fredericks HF, Zelzion E, Knowles B, Murat Eren A, Vandzura R, Laber CP, Schieler BM, Johns CT, More KD, Coolen MJL, Follows MJ, Bhattacharya D, VanMooy BAS, Bidle KD (2019) Biogeochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology. Environmental Microbiology doi:10.1111/1462-2920.14633

Johns CT, Grubb A., Nissimov JI, Natale F, Knapp V, Mui A, Fredricks H, Van Mooy BAS & Bidle KD (2018) ‘The mutual interplay between calcification and coccolithovirus infection in Emiliania huxleyi’, Environmental Microbiology, doi:10.1111/1462-2920.14362.

Laber CP, Hunter JE, Carvalho AF, James R. Collins JR, Hunter E, Schieler B, Boss E, More K, Frada M, Thamatrakoln K, Brown CM, Haramaty L, Ossolinski J, Fredricks H, Nissimov JI, Gardella R, Sheyn U, Lehahn Y, Chant RJ, Martins AM, Coolen MJL, Vardi A, DiTullio GR, Van Mooy BAS & Bidle KD (2018) ‘Coccolithovirus stimulation of carbon export in the North Atlantic’’, Nature Microbiology, 3, 537-547.

Nissimov JI, Vandzura R, Johns CT, Haramaty L, Natale F & Bidle KD (2018) ‘Dynamics of transparent exopolymer particle (TEP) production and aggregation during viral infection of the coccolithophore, Emiliania huxleyi, Environmental Microbiology, doi:10.1111/1462-2920.14261.

Thompson LR et al. and The Earth Microbiome Project Consortium (2017) ‘A communal catalogue reveals Earth’s multiscale microbial diversity’ Nature, 551, 457-463.

Nissimov JI & Bidle KD ‘Stress, death, and the biological glue of sinking matter’ (2017) Journal of Phycology, 53 (2), 241–244.

Nissimov JI, Pagarete A, Ma F, Cody S, Dunigan DD, Kimmance SA & Allen MJ (2017) ‘Coccolithoviruses: a review of genomic thievery and metabolic thuggery’ Viruses, 9 (3), 52; doi:10.3390/v9030052.

Nissimov JI, Napier JA, Allen MJ & Kimmance SA (2016) ‘Intragenus competition between coccolithoviruses: an insight on how a select few can come to dominate many’ Environmental Microbiology, 18 (1), 133–145.

Nissimov JI, Napier JA, Kimmance SA & Allen MJ (2014) ‘Permanent draft genomes of four new coccolithoviruses: EhV-18, EhV-145, EhV-156 and EhV-164’ Marine Genomics, 15: 7-8. 

Nissimov JI, Jones M, Napier JA, Munn CB, Kimmance SA & Allen MJ (2013) ‘Functional inferences of environmental coccolithovirus biodiversity’ Virologica Sinica, 28 (5): 291-302.

Sperling M, Piontek J, Gerdts G, Wichels A, Schunck H, Roy A-S, La Roche J, Gilbert J, Nissimov JI, Bittner L, Romac S, Riebesell U & Engel A. (2013) ‘Effect of elevated CO2 on the dynamics of particle-attached and free-living bacterioplankton communities in an Arctic fjord’ Biogeosciences, 10: 181-191.

Roy A-S, Gibbons SM, Schunck H, Owens S, Caporaso JG, Sperling M, Nissimov JI, Romac S, Bittner L, Riebesell U, LaRoche J & Gilbert JA (2013) ‘Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms’ Biogeosciences, 10: 555-566.

Allen MJ, Tait K, Mühling M, Weynberg K, Bradley C, Trivedi U, Gharbi K, Nissimov JI, Mavromatis K, Jensen CN, Grogan G & Ali ST (2012) ‘Genome Sequence of Stenotrophomonas maltophilia PML168, Which Displays Baeyer-Villiger Monooxygenase Activity’ Journal of Bacteriology, 194 (17): 4753-4754.

Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H & Allen MJ (2012) ‘Draft genome sequence of the coccolithovirus EhV-202’ Journal of Virology, 86 (4): 2380-2381.

Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H & Allen MJ (2012) ‘Draft genome sequence of four coccolithoviruses: EhV- 88, EhV- 201, EhV-207 and EhV-208’ Journal of Virology, 86 (5): 2896-2897.

Nissimov JI, Worthy CA, Rooks P, Napier JA., Kimmance SA, Henn MR, Ogata H & Allen MJ (2011) ‘Draft genome sequence of the coccolithovirus EhV-84’ Standards in Genomic Sciences, 5: 1-11

Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H & Allen MJ (2011) ‘Draft Genome Sequence of the Coccolithovirus Emiliania huxleyi Virus 203’ Journal of Virology, 85 (24): 13468–13469.

Nissimov J, Rosenberg E & Munn CB (2009) ‘Antimicrobial properties of resident coral mucus bacteria of Oculina patagonica’ FEMS Microbiology Letters, 292: 210–215.

 

Other publications 

James L. Van Etten, David D. Dunigan, Keizo Nagasaki, Declan Schroeder, Nigel Grimsley, Corina P.D. Brussaard and Jozef I. Nissimov 'Phycodnaviruses (Phycodnaviridae)'. Co-authorship contribution towards a book chapter on algal viruses for the Fourth edition of the Encyclopedia of Viruses (in review).

I arrived at SAMS early in 2019 and have not yet taken on teaching responsibilities. However, I will taken on teaching Marine Microbiology later this year, which will include several lectures and laboratory practicals.

 

Past teaching experience

Invited lectures in the US and UK (2013-18) and course developer for undergraduate students at Rutgers University (USA) titled 'Ocean science inquiry' 2017-18

 

Alumni research students 

Alwin Mui: Calcification and exopolymeric particle production in Emiliania huxleyi at nitrate-limiting conditions. BSc (Hons) project 2017-18. Department of Marine and Coastal Sciences, Rutgers University, NJ (USA)

Kevin Ma: Can marine viruses stimulate phytoplankton growth and survival under environmental stress? BSc (Hons) project 2016-17. Department of Marine and Coastal Sciences, Rutgers University, NJ (USA)

Lauren Palena: The impact of nitrogen and phosphorous limitation on host fitness and viral production in the Emiliania huxleyi - Coccolithovirus model system. BSc (Hons) project 2016-17. Department of Marine and Coastal Sciences, Rutgers University, NJ (USA)

Rebecca Gardella-Vandzura: Elucidating the interplay between transparent exopolymeric particle production and cell aggregation during viral infection of the coccolithophore, Emiliania huxleyi. BSc (Hons) project 2015-16. Department of Marine and Coastal Sciences, Rutgers University, NJ (USA)

Expert advice to regulators / government

Grant proposal reviewer for the National Science Foundation (NSF) of the USA Biological Oceanography program

 

Research expeditions

2017: Mesocosm experiment in the Norwegian fjords of Bergen, Norway

2015: Scientific cruise at Station ALOHA (Hawaii) on board R/V Kilo Moana, in collaboration with the Centre for Microbial Oceanography: Research and Education (CMORE) at the University of Hawaii at Manoa

2014: Central California Current System (CCS) diatom cruise onboard the R/V Melville

2010-11: Collaborative project with the British Antarctic Survey (BAS) at Rothera research station, Adelaide Island, Antarctica 

2010: Atlantic Meridional Transect 20 (AMT 20). A 46-day research cruise from Southampton (UK) to Punta Arenas (Chile) onboard the NERC ship RRS James Cook

2010: European Project on Ocean Acidification (EPOCA): Arctic Campaign. A mesocosm experiment in the Fjord near Ny-Alesund Research Station, Svalbard, conducted in collaboration with scientists from more than 30 countries

 

Outreach/public engagement

2015 - 2018: Development of short videos about marine science as an educational tool for children aged 12-18 (as part of a 2015 NSF funded grant and the national Next Generation Teaching Standards in the USA). http://toolsofscience.org/index.html

2014 & 2018 Science judge for the annual Shore Bowl competition in New Jersey, USA (a regional academic competition for high school students in NJ, NY, and PA that focuses on ocean-related topics).

2011 Nissimov J. “With James Cook on the Atlantic Meridian” Objects 9 (27): 10-14 (article in a Bulgarian popular science magazine).

2010 Nissimov J. “Moments from the country of the midnight sun” Objects 11(17): 54-59 (article in a Bulgarian popular science magazine).

 

Professional memberships

Since 2013: Member of The International Society for Viruses of Microorganisms (ISVM)

Since 2012: Member of Association for the Sciences of Limnology and Oceanography (ASLO)

 

Other professional responsibilities 

Review Editor for: Frontiers in Microbiology and Frontiers in Marine Science

Ad hoc journal reviewer for: PNAS, PlosOne, Environmental Microbiology, FEMS Microbiology, Journal of Plankton Research, Viruses, Virologica Sinica, Virus Genes, Deep Sea Research Part I  

2015-16: Member of the Website Advisory Team for the Office of Postdoctoral Affairs at Rutgers University, USA 

2011-13 Committee member of a discussion panel funded by the MOORE Foundation for the development of an online science resource - VERVE Net (the Viral Ecology Research and Virtual Exchange Network)

Employment history

Since 2019: Lecturer in Microbial Oceanography. SAMS (UK)

2013-18: Postdoctoral Research Associate. Department of Marine and Coastal Sciences, Rutgers University (USA)

2013: Research Assistant. Department of Plant Sciences, Oxford University (UK)

2008-12: Marine Microbiology Laboratory Teaching Assistant (part-time). University of Plymouth (UK)

 

Other affiliations

Since 2018: Guest Scientist at the Department of Marine and Coastal Sciences, Rutgers University (USA)

2014-15: Guest Investigator at the Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution (USA)

 

Education qualifications

2013 PhD Biosciences. The University of Nottingham (UK) in partnership with the Plymouth Marine Laboratory

2009 MRes Marine Biology. University of Plymouth (UK) in partnership with the Marine Biological Associciation of the UK

2008 BSc (Hons) Marine Biology. University of Plymouth (UK)