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. Current projects concern molecular identification of fish larvae and their prey.

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.

Recent publications

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

Research projects

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: 6.37 mill. Danish Kr.

Brief Summary: The import of nitrogen (N) through biological N₂fixation 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 N₂fixing 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.

Master and Bachelor projects

Previous students and postdocs

Previous PhD students (Riemann main supervisor)

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

Previous PostDocs

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)

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 August 2020. From left: Subhendu Chakraborty, Ellen Salamon, Lasse Riemann, Meriel Bittner, Tobias Launbjerg, Lisa W. von Friesen, and Søren Hallstrøm.

Members

Name	Title	Phone	E-mail
Ellen Rachel Salamon	Paid by the hour	+45 353-32245	E-mail
Lasse Riemann	Professor	+45 353-21959	E-mail
Lisa Winberg von Friesen	PhD fellow	+45 353-32787	E-mail
Meriel Jennifer Bittner	PhD fellow	+45 353-33744	E-mail
Subhendu Chakraborty	Postdoc	+45 353-31567	E-mail
Søren Hallstrøm		+45 353-31089	E-mail

Other members

Name	Title

Contact

Professor Lasse Riemann
Head of Marine Biological Section
Professor in Marine molecular microbiology

Marine Biological Section
Strandpromenaden 5
DK-3000 Helsingør, Denmark

Researcher ID
Phone: +45 35 32 19 59
Email: lriemann@bio.ku.dk

News

New 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 becom 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). In press. Frontiers in Marine Science