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.
Benavides M, Duhamel S, Van Wambeke F, Shoemaker KM, Moisander PH, Salamon E, Riemann L, Bonnet S. Dissolved organic matter stimulates N2 fixation and nifH gene expression in natural Trichodesmium colonies. In press. FEMS Microbiol Letters
2020. Alneberg J, Bennke C, Beier S, Bunse C, Quince C, Ininbergs K, Riemann L, Ekman M, Jürgens K, Labrenz M, Pinhassi J, Andersson AF. Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes. Communications Biology 3, Article 119 (Open access)
2019. Tang KW, Backhaus L, Riemann L, Koski M, Grossart H-P, Munk P, Nielsen TG. Copepod carcasses in the Subtropical Convergence Zone of the Sargasso Sea: Implications for microbial community composition, system respiration and carbon flux. J. Plank. Res. 41(4): 549-560
2019. Happel EM, Markussen T, Teikari J, Huchaiah V, Alneberg J, Andersson AF, Sivonen K, Middelboe M, Kisand V, Riemann L. Effects of allochthonous DOM input on microbial composition and nitrogen cycling genes at two contrasting estuarine sites. FEMS Microbiology Ecology, 95, fiz123
2019. Lundgreen RBC, Jaspers C, Traving SJ, Ayala DJ, , Lombard F, Grossart H-P, Nielsen TG, Munk P, Riemann L. Eukaryotic and cyanobacterial communities associated with marine snow particles in the oligotrophic Sargasso Sea. Scientific Reports, 9:8891
2019. Richert I, Yager P, Dinasquet J, Logares R, Riemann L, Wendeberg A, Bertilsson S, Scofield. Summer comes to the Southern Ocean: how phytoplankton shape bacterioplankton communities far into the deep dark sea. Ecosphere, 10(3): e02641
2019. Charvet S, Riemann L, Alneberg J, Andersson A, von Borries J, Fischer U, Labrenz M. AFISsys - an autonomous instrument for the preservation of brackish water samples for microbial metatranscriptome analysis. Water Research, 149:351-361
2019. Olofsson M, Torstensson A, Karlberg M, Steinhoff FS, Dinasquet J, Riemann L, Chierici M, Wulff A. Limited response of a spring bloom community inoculated with filamentous cyanobacteria to elevated temperature and pCO2. Botanica Marina, 62(1): 3-16
2019. Swalethorp R, Dinasquet J, Logares R, Bertilsson S, Kjellerup S, Krabberød AK, Moksnes P-O, Nielsen TG, Riemann L. Microzooplankton distribution in the Amundsen Sea Polynya (Antarctica) during an extensive Phaeocystis antarctica bloom. Progress in Oceanography, 170: 1-10
2018. Inomura K, Bragg J, Riemann L, Follows MJ. A quantitative model of nitrogen fixation in the presence of ammonium. PLOS One, 13(11): e0208282
2018. Pedersen JN, Bombar D, Paerl RW, Riemann L. Diazotrophs and N2-fixation associated with particles in coastal estuarine waters. Frontiers in Microbiology, 9:2759
2018. Paerl RW, Sundh J, Tan D, Svenningsen SL, Hylander S; Andersson AF, Pinhassi J, Riemann L. Prevalent reliance of bacterioplankton on exogenous vitamin B1 and precursor availability. Proc. Natl. Acad. Sci. USA, 115(44):E10447-E10456
2018. Markussen T, Happel EM, Teikari J, Huchaiah V, Alneberg J, Andersson A, Sivonen K, Riemann L, Middelboe M, Kisand V. Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change. Environmental Microbiology, 20(8):3083-3099
2018. Happel E, Bartl I, Voss M, Riemann L. Extensive nitrification and active ammonia oxidizers in two contrasting coastal systems of the Baltic Sea. Environmental Microbiology, 20(8):2913-2926
2018. Munk P, Nielsen TG, Jaspers C, , Ayala DJ, Tang KW, Lombard F, Riemann L,. Vertical structure of plankton communities in areas of European eel larvae distribution in the Sargasso Sea. J. Plankton. Res. 40(4):362-375
2018. Alneberg J, Sundh J, Bennke C, Beier S, Lundin D, Hugerth LW, Pinhassi J, Kisand V, Riemann L, Jürgens K, Labrenz M, Andersson AF. BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea. Scientific Data, 5:180146
2018. Shiozaki T, Bombar D, Riemann L, Sato M, Hashihama F, Kodama T, Tanita I, Takeda S, Saito H, Hamasaki K, Furuya K. Linkage between dinitrogen fixation and primary production in the oligotrophic South Pacific Ocean. Global Biogeochemical Cycles, 32:1028-1044
2018. Rowe OF, Dinasquet J, Paczkowska J, Figueroa D, Riemann L and Andersson A. Major differences in dissolved organic matter characteristics and bacterial processing over an extensive brackish water gradient, the Baltic Sea. Marine Chemistry, 202: 27-36
2018. Ayala DJ, Munk P, Lundgreen RBC, Traving SJ, Jaspers C, Jørgensen TS, Hansen LH, Riemann L. Gelatinous plankton is important in the diet of European eel (Anguilla anguilla) larvae in the Sargasso Sea. Scientific Reports, 8: 6156
2018. Paerl RW, Bertrand E, Rowland E, Scatt P, Mehiri M, Niehaus T, Hanson AD, Riemann L, Yves-Bouget F. Carboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis. Scientific Reports, 8: 5940
2018. Benavides M, Bonnet S, Berman-Frank I, Riemann L. Deep into oceanic N2 fixation. Frontiers in Marine Science, 5:108
2018. Paerl RW, Hansen T, Henriksen NNSE, Olesen AK, Riemann L. N-fixation and related O2 constraints on model marine diazotroph Pseudomonas stutzeri BAL361. Aquat. Microb. Ecol., 81: 125-136
2018. Wulff A., Karlberg M., Olofsson M., Torstensson A., Riemann L., Steinhoff F., Mohlin M., Ekstrand N., Chierici M.. Ocean acidification and desalination - Climate-driven change in a Baltic Sea summer microplanktonic community. Marine Biology, 165 (4):63
2018. Bombar D, Paerl RW, Anderson R, Riemann L. Filtration via conventional GF/F -filters in 15N2 tracer assays fails to capture all nitrogen-fixing prokaryotes. Frontiers in Marine Science 5:6
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
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.
Nitrogen fixation and ecology of heterotrophic bacteria in coastal temperate waters
Financed by: The Danish Council for Independent Research, 2017-2022
PI: Lasse Riemann
Total budget: 854,000 Euro
Brief Summary: The import of nitrogen (N) through biological N2 fixation is essential for life in vast areas of the global ocean. The prevailing belief is that cyanobacteria using light are the only relevant N2 fixing organisms and that N2 fixation in coastal temperate waters is negligible. It has, however, now become evident that heterotrophic N2 fixing bacteria with a fundamentally different ecology are widespread and active in marine waters, and that they can do high N2 fixation in coastal waters. This cross-disciplinary project using cultivation, field and modeling approaches aims to establish knowledge on the ecology of heterotrophic N2 fixing bacteria, quantify rates and factors controlling their N2 fixation, and integrate these data into N budgets of coastal temperate waters. A significant N input from this novel group of N2 fixers will establish a new paradigm in N2 fixation research, and have broad implications for our understanding of the N and carbon cycling in coastal temperate waters.
Vitamin B1 limitation of bacterioplankton in coastal temperate waters
Financed by: Independent Research Fund Denmark, 2019 - 2022
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.
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. 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.
|Ellen Salamon||Master student|
|Pernille Fornitz Marloth||Master student|
Professor Lasse Riemann
Professor in Marine molecular microbiology
Marine Biological Section
DK-3000 Helsingør, Denmark
Congratulations to Søren Hallstrøm with his successful PhD defense 29 January.
January 2020. 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 2020. 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.
Saulia, E., Benavides, M., Henke, B.A, Turk-Kubo, K.A, Cooperguard, H., Grosso, O., Desnues A., Rodier, M., Dupouy, C., Riemann, L., Bonnet, S.Seasonal shifts in diazotroph players: patterns observed over a two-year time series in the New Caledonian lagoon (Western Tropical South Pacific Ocean). Frontiers in Marine Science
Benavides M, Duhamel S, Van Wambeke F, Shoemaker KM, Moisander PH, Salamon E, Riemann L, Bonnet S. Dissolved organic matter stimulates N2 fixation and nifH gene expression in natural Trichodesmium colonies. 2020. FEMS Microbiol Letters 367, fnaa034