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 projects and jobs”: https://karriere.ku.dk/da/projects/danmark for examples and inspiration for possible projects.
Previous PhD students (Riemann main supervisor)
- Søren Hallstrøm. “Nitrogen fixation in marine waters: Importance of environmental gradients”. PhD degree 01.2021. Email
- Elisabeth Münster Happel, "The effects of riverine DOM on microbial composition and function". PhD degree 24 August 2018. Email
- Daniel Jiro Ayala, "The early life of the European eel in the ichthyoplankton community of the Sargasso Sea". Main supervisor: Peter Munk. Co-supervisor: Lasse Riemann. PhD degree 27 October 2016. Email
- Sachia Jo Traving, "Traits for bacterial carbon turnover in the marine environment: chemical complexity meets bacteria diversity". PhD degree 24 June 2016. Email
- Mikkel Bentzon-Tilia, "The Biology of heterotrophic nitrogen fixing bacteria in marine and estuarine waters". PhD degree 25. April 2014. Email
- Julie Dinasquet, "Top-down and bottom-up control of bacterial activity and community structure". PhD degree 13. March 2013, Linnaeus University, Sweden. Email
- Hanna Farnelid, "Distribution and activity of nitrogen fixing bacteria in marine and estuarine waters". PhD degree 25 January 2013, Linnaeus University, Sweden.
- Johanna Sjösted, "Effect of environmental factors on bacterioplankton community composition, diversity and functionality". PhD degree 1. February 2013, Linnaeus University, Sweden. Email
- Karin Holmfeldt "Regulation of bacterioplankton community composition - emphasis on viruses". Ph.D. degree 21 August 2009
- Kjärstin Hagman Boström "Nitrogen fixation by heterotrophic bacterioplankton in the Baltic Sea". Ph.D. degree 20 January 2006, University of Kalmar
- Cecilia Leitet "Plasmids and prophages in Baltic Sea Bacterioplankton". Filosofie Licentiat 27 January 2006, University of Kalmar
- Dr. Subhendu Chakraborty, PostDoc. "Modelling particle-associated nitrogen fixation". 04-2019-12-2020. Email
Dr. Mar Benavides, PostDoc. "Ecology of heterotrophic N2 fixing bacteria in marine coastal waters". 01-2017 - 06-2018. Email
Dr. Deniz Bombar, PostDoc. "Nitrogen fixing heterotrophic bacteria in coastal waters". 03-2014 - 06-2018. Email
Dr. Sachia Jo Traving, PostDoc. "Interactions between dissolved organic matter and bacterioplankton in marine waters". 06-2016 - 2018. Email
Dr. Ryan Paerl, PostDoc. "Ecophysiological adaptations of planktonic microbes". Started: 10-2014 - 12-2016. Email
Dr. Sophie Charvet, PostDoc. "Development of an autonomous multisampler system for pelagic RNA sampling". 10-2014 - 08-2015. Associated with the AFISmon project. Email
Dr. Ina Severin, "Ecology of heterotrophic nitrogen-fixing prokaryotes in marine waters". 06-2012 - 06-2014. Email
Dr. Claudia Dziallas. "Evolution of symbiosis between ciliates and nitrogen-fixing prokaryotes " Marie Curie fellow. 01-2012 - 05-2014. Email
Dr. Julie Dinasquet. "Bacterioplankton community composition and succession" 2013. Email
Dr. Dusko Odic. Working on virus-host interactions and X-ray crystallography. The project was a collaboration with Prof. Janos Hajdu, University of Uppsala, Sweden. 2008-2009.
Previous Master students (Riemann main supervisor)
- Tobias Launbjerg, "Identity and activity of heterotrophic nitrogen fixing bacteria in resuspended sediments of the coastal Baltic Sea". Master degree 09-2020.
- Mads Obi Bergsten, "Composition and expression of ammonia oxygenase genes in two river outlets in the Baltic Sea". Master degree: 05-2017.
- Jeppe Nedergaard Pedersen, "Organic particles as hotspots for nitrogen fixation by marine heterotrophic bacteria". Master degree March 2017
- Regitze B C Lundgreen, "Marine snow particles in the oligotrophic Sargasso Sea as analysed by PCR amplicon sequencing: composition and linkage to the plankton". Master degree December 2016
- Liv Louise Victoria Backhaus, "Microbial decomposition of copepod carcasses in surface waters of the oligotrophic Sargasso Sea". Master degree January 2016
- Elisabeth Münster Happel, "Nitrogen fixation in the Baltic Sea - diurnal and vertical patterns". Mater degree June 2014. University of Copenhagen
- Daniel Jiro Ayala , "Diversity of fish larvae communities across the subtropical convergence zone of the Sargasso Sea". Master degree February 2012. Danish Technical Univ.
Hanna Alfredsson "Prey Selection of European Eel ( Anguilla anguilla ) Larvae in the Sargasso Sea: a Molecular Approach". Master degree September 2009, University of Kalmar.
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.
|Lisa Winberg von Friesen||PhD Fellow||+4535332787|
|Stine Zander Hagen||PhD Fellow||+4535329150|
|Vasiliki Papazachariou||PhD Fellow||+4535321675|
|Victor Fernandez Juarez||Postdoc||+4535320317|
|Jiaqi Wang||Master student|
|Signe DM Pedersen||Master student|
Professor Lasse Riemann
Professor in Marine molecular microbiology
Marine Biological Section
DK-3000 Helsingør, Denmark
Phone: +45 35 32 19 59
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: https://doi.org/10.3389/fmicb.2022.869093
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. N2 fixation 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. https://employment.ku.dk/faculty/?show=153345
January 2021. 3-year PhD position available on marine nitrogen fixation
Deadline for application 2. February; tentative start 1. April 2021. https://employment.ku.dk/phd/?show=153313
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.