Marine Molecular Microbiology

The research interests of the group concern marine microbial ecology. We apply molecular and microbiological tools to identify factors that regulate bacterioplankton community composition in the ocean. Recent and ongoing projects are especially related to the ecology of heterotrophic N2-fixing bacterioplankton and bacterial diversity and population dynamics.

In parallel with the microbiology projects, we apply molecular tools in projects adressing aspects of plankton ecology. 

Standard microbiology techniques and bacterial cultivation are combined with state-of-the-art molecular methodology such as: PCR, Real-Time PCR, metagenomics, transcriptomics and amplicon sequencing. Approaches include field work as well as experimental work.


Nitrogen fixation in a changing Arctic ocean: an overlooked source of nitrogen?

Financed by: Independent Research Fund Denmark, 2023-2025

PI: Lasse Riemann; Collaborators: Colin Stedmon (DTUaqua) and Takuhei Shiozaki (Univ. Tokyo, Japan)

Budget: 386,600 Euro

Brief Summary: Since primary production in the Arctic Ocean (AO) is limited by nitrogen (N) availability, knowledge about sources and sinks of N is of critical importance. Surprisingly, a few recent studies have presented sporadic data suggesting N2 fixation in the AO. This import of bioavailable N could be of fundamental importance for N and carbon biogeochemistry in the AO, but data are scarce. This cross-disciplinary and international project aims to quantify pelagic N2 fixation in the AO – a biological process hitherto unaccounted for. In situ measurements, experiments, and use of cutting-edge methodology will provide unprecedented data on fixation rates, identity of the active organisms, and insights into controlling factors in a cross-Arctic Ocean survey. This information is essential for prediction of primary production in the future AO, particularly in the face of climate change.

Future stimulated nitrogen fixation: threatening the health of coastal ecosystems?

Financed by: Independent Research Fund Denmark, 2021-2024

PI: Lasse Riemann; Co-PI: Caroline Löscher (SDU) and Stiig Markager (AU)

Budget: 829,419 Euro

Brief Summary: Nitrogen (N) is often the limiting factor for plankton productivity in coastal waters. N2 fixation is a globally important process in marine waters, and sporadic data document such fixation from Danish waters. Nevertheless, despite eutrophication may be critically impacted by N supply via N2 fixation, data on the extent, regulation, and importance of this process does not exist for Danish waters. This is a prerequisite for an efficient and sustainable environmental management – in particular, because climate change is predicted to increase the future magnitude and relative importance of N2 fixation in our waters. In the proposed project, field and experimental work will systematically quantify N2 fixation in Danish waters and sediments, identify the organisms responsible, and determine the factors regulating the process. These data will feed a model on pools, sources, sinks and fluxes of N providing vital information for future Danish environmental management of coastal marine waters.

Pathogenic Vibrio bacteria in the current and future Baltic Sea waters: mitigating the problem (BaltVib)

Financed by: The Danish Council for Independent Research under the EU COFUND call "Biodiversity and Climate change", 2021-2023

Co-PI: Lasse Riemann (Coordinator: Prof. Matthias Labrenz, IOW, Germany)

UCPH budget: 301,277 Euro

Brief Summary: Vibrio – microbes that are part of the natural bacterioplankton in temperate marine waters – have in recent years flourished in the Baltic Sea, probably stimulated by elevated surface water temperatures. Several Vibrio species are human pathogens. It is hence of great concern that Vibrio-related wound infections and fatalities have increased dramatically along the Baltic coasts. Future climate change is predicted to escalate this problem, posing a significant threat to human health and the Baltic tourism industry. However, the projections do not yet take into account the influence of ‘ecosystem engineers’ such as mussels and macrophytes on Vibrio diversity and abundance. Recent data indicate that in some of the ‘ecosystem engineers’ habitats the abundance of pathogenic Vibrio spp. is reduced. This opens up the option for nature-based solution (NbS) strategies to control pathogenic vibrios in the nearshore habitat where humans interact with the sea. However, climate change will also affect the structure and functioning of the ecosystem engineers, with as yet unknown consequences for the Vibrio populations in the Baltic Sea. BaltVib aims to delineate the current and future Vibrio status, determine biotic and abiotic key factors regulating Vibrio prevalence, and identify NbSs to mitigate the problem. This will be accomplished through interdisciplinary integration of marine, microbiological, molecular and socioecological expertise carried by partners from seven Baltic nations.

Vitamin B1 limitation of bacterioplankton in coastal temperate waters

Financed by: Independent Research Fund Denmark, 2019 - 2023

PI: Lasse Riemann; Co-PIs: Ryan Paerl, Anders Andersson

Total budget: 385,000 EURO 

Brief summary: Vitamin B1 is a required nutrient for virtually all cells, yet is produced by only a small subset. In recent breakthrough work, we showed that B1/precursor bioavailability periodically limits bulk growth of bacterioplankton in the Baltic Sea. Moreover, via metagenomics analyses, we show that B1-auxotrophy is widespread amongst wild bacterioplankton around the globe. In the proposed project, field and experimental work in estuaries on both sides of the Atlantic Ocean, and cultivation work, will be integrated to test the hypothesis that: “Vitamin B1 is a hitherto overlooked factor that significantly influences bacterioplankton growth and community dynamics in coastal temperate waters”. This would constitute a paradigm shift with implications for our perception of microbial nutrient cycling, but also with ramifications for productivity of higher trophic levels, and ultimately for our understanding and management of temperate estuaries as resources and recipients.









Please visit “UCPH Jobteaser” (please log in with UCPH credentials) for examples and inspiration for possible projects.


















The Riemann group, March 2023. From left: Vasiliki Papazachariou, Jiaqi Wang, Amalie K. Jensen, Lisa von Friesen, Sissel M. Iversen, Lasse Riemann, Sebastian Boysen Kjær, Selma M. Kuypers, Nanna M. Christiansen, Stine Zander Hagen and Víctor Fernández Juárez.
Meriel Bittner was not present.


Name Title Phone E-mail
Eve Isobel Galen PhD Student +4535334676 E-mail
Lasse Riemann Professor +4535321959 E-mail
Stine Zander Hagen PhD Fellow +4535329150 E-mail

Other members

Name Title
Emma Nysted Christophersen Master project student
Bjarke Heilskov Kristensen Master project student
Nanna Meilholm Christiansen Master project student
Marie Neel Jørgensen Master project student
Signe DM Pedersen Master project student


Professor Lasse Riemann
Professor in Marine molecular microbiology

Marine Biological Section
Strandpromenaden 5
DK-3000 Helsingør, Denmark

Researcher ID
Phone: +45 35 32 19 59


January 2024. Congratulations to Alba and Kasper with the acceptance of our collaborative publications in Limnology and Oceanography Letters and Microbiology spectrum:

Filella A, Umbricht J, Klett A; Vogts A, Vannier T, Grosso O, Voss  M,  Riemann L, Benavides M. DOM offsets the detrimental effects of climate change in the nitrogen fixing cyanobacterium Crocosphaera. Limnology and Oceanography Letters

Brodersen KA, Mosshammer M, Bittner MJ, Hallstrøm S, Santner J, Riemann L, Kühl M. Seagrass-mediated rhizosphere redox gradients are linked with ammonium accumulation driven by diazotrophs. Microbiology Spectrum

December 2023. Congratulations Meriel with the acceptance of our paper in ISME Communications: New chemical and microbial perspectives on vitamin B1 and vitamer dynamics of a coastal system. Bittner MJ, Bannon CC, Rowland E, Sundh J, Bertrand EM, Andersson AF, Paerl RW, Riemann L. 

November 2023. Congratulation Victor, Cesar and all for the beautiful cover photo on the new issue of Applied and Environmental Microbiology - and for making it into "Articles of Significant Interest in This Issue" (AEM Table of Contents Volume 89, Issue 11 ( Biofilm formation and cell plasticity drive diazotrophy in an anoxygenic phototrophic bacterium. By Fernández-Juárez V, Hallstrøm S, Pacherres CO, Wang J, Coll-Garcia G, Kühl M, and Riemann L.

13 October 2023. Congratulation Ellen with the acceptance of our paper in Estuarine, Coastal and Shelf Science: Composition and distribution of diazotrophs in the Baltic Sea. Salamon Slater ER, Turk-Kubo KA, Hallstrøm S, Kesy K, Laas P, Magasin J, Zehr JP, Labrenz M, Riemann L. 

15 September 2023. Congratulation Victor with the acceptance of our paper in Applied and Environmental Microbiology: Biofilm formation and cell plasticity drive diazotrophy in an anoxygenic phototrophic bacterium. Fernández-Juárez V, Hallstrøm S, Pacherres CO, Wang J, Coll-Garcia G, Kühl M, Riemann L.

8 September 2023. Congratulations Meriel Bittner, for successfully defending your PhD thesis "Vitamin B1 dynamics in coastal waters" in front of the opponents Prof. Justin Seymour, Prof. Eva Teira, and Prof. M. Middelboe.

August 2023. The revised Luo database paper now came out. A very valuable compilation of nitrogen fixation rates as well as other data. Earth System Science Data

June 2023. Congratulations to Lisa with the acceptance of her paper: Glacial meltwater and seasonality influence community composition of diazotrophs in Arctic coastal and open waters. Von Friesen L, Paulsen M, Müller O, Gründger, F, Riemann L. In Press, FEMS Microbiology Ecology

December 2022. New paper accepted on the importance of resuspension for pelagic N2 fixation: Liesirova T, Aarenstrup-Launbjerg T, Hallstrøm S, Bittner MJ, Riemann L, and Voss M. Nitrogen-fixing sulfate reducing bacteria in shallow coastal sediments under simulated resuspension. In Press, Estuarine coastal and shelf science 

November 2022. We just had two papers accepted:
- Zehr JP, Riemann L. Quantification of gene copy numbers is valuable in marine microbial ecology; a comment to Meiler et al. (2022). In Press Limnology and Oceanography 
- Pinhassi J, Farnelid HM, Martínez-García S, Teira E, Galand PE, Obernosterer I, Quince C, Vila-Costa M, Gasol JM, Lundin D, Andersson AF, Labrenz M and Riemann L. Functional responses of key marine bacteria to environmental change - towards genetic counselling for coastal waters. Frontiers in Microbiology:

August 2022. Søren's chemotaxis paper now available online in ISME J. Hurra: Hallstrøm S, Raina J-B, Ostrowski M, Parks DH, Tyson GW, Hugenholtz P, Stocker R, Seymour JR, Riemann L. Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean. ISME J

25 July 2022. Filella A, Riemann L, Van Wambeke F, Pulido-Villena E, Vogts A, Bonnet S, Grosso O, Diaz JM, Duhamel S and Benavides M. Contrasting roles of DOP as a source of phosphorus and energy for marine diazotrophs. Frontiers in Marine Science, 9:923765

July 2022. Paper accepted in ISME J on N2 fixation in the deep ocean by Trichodesmium. Benavides M, Bonnet S, Le Moigne FAC, Armin G, Inomura K, Hallstrøm S, Riemann L, Berman-Frank I, Poletti E, Garel M, Grosso O, Leblanc K, Guigue C, Tedetti M, Dupouy C. Sinking Trichodesmium fixes nitrogen in the dark ocean. ISME J, in press 

4 May 2022. Hallstrøm S, Benavides M, Salamon ER, Arístegui J, Riemann L. Activity and distribution of diazotrophic communities across the Cape Verde Frontal Zone in the Northeast Atlantic Ocean. Biogeochemistry, published online  

6 April 2022. New mini-review out: Riemann L, Rahav E, Passow U, Grossart H-P, de Beer D, Klawonn I, Eichner E, Benavides M, Bar-Zeev E. Planktonic aggregates as hotspots for heterotrophic diazotrophy: the plot thickens. Frontiers in Microbiology 13:875050

13 December 2021. New paper available online in Limnology and Oceanography: Hallstrøm S, Benavides M, , Salamon E, Evans CW, Potts LJ, Granger J, Tobias CR, Moisander PH, Riemann L. Pelagic N2 fixation dominated by sediment diazotrophic               communities in a shallow temperate estuary

1 December 2021. New paper in press in Biogeosciences: Ridame C, Dinasquet J, Hallstrøm S, Bigeard E, Riemann L, Van Wambeke F, Bressac M, Pulido-Villena E, Taillandier V, Gazeau F, Tover-Sanchez A, Baudoux A-C, Guieu C. Nfixation in the Mediterranean Sea related to the composition of the diazotrophic community, and impact of dust under present and future environmental conditions

27 July 2021. Congrats to Subhendu. Our paper was now chosen for the Editors' highlights page in Nature Communications.

17 July 2021. Lisa is soon leaving on a 2 month cruise to the North Pole. See press release

2. July 2021. Congrats to Subhendu with our new paper in Nature Communications on particle-associated N2 fixation. See also our press release.

May 2021. Welcome to postdoc Víctor Fernández Juárez and PhD student Vasiliki Papazachariou in our group.

Congratulations to Søren Hallstrøm with his successful PhD defense 29 January.

January 2021. 2-year Postdoc position available on marine bacterial community composition with special emphasis on pathogenic Vibrios.
Deadline for application is 17. February; tentative start 1. April 2021.

January 2021. 3-year PhD position available on marine nitrogen fixation
Deadline for application 2. February; tentative start 1. April 2021.

Nov. 2020, Lisa's mini-review on Arctic nitrogen fixation is now published: von Friesen, L.W, Riemann, L. Nitrogen fixation in a changing Arctic Ocean: An overlooked source of nitrogen? Frontiers in Microbiology, 11: 596426

Nov. 2020: New DFF-project funded: Future stimulated nitrogen fixation: threatening the health of coastal ecosystems?”. PI of this four-year EU project fundet by Independent Research Fund, Denmark. From spring 2021, a three-year PhD position will become available in our group. 

Oct 2020: New EU-project funded: Pathogenic Vibrio bacteria in the current and future Baltic Sea waters: mitigating the problem (BaltVib)”. Partner in this three-year EU project fundet by the Biodiversa program. A two-year postdoc postion will become available in our group, starting in spring 2021.