Biological lenses using gene prints
Prokaryotic microbes are principal drivers of carbon and nutrient biogeochemistry and account for a major fraction of pelagic biomass and productivity in the Baltic Sea. Still, these organisms are neither included among the indicators of environmental status currently in use nor considered as functional entities in biogeochemical models. This flaw has been highlighted by HELCOM and OSPAR in their work to coordinate the development of indicators and determining GES in the Baltic and North Sea areas. The last decade has witnessed a tremendous increase in the capacity of high-throughput technologies for retrieving and processing genetic information from environmental samples; this has given mechanistic understanding of microbially driven food-web processes and how microbes are affected by environmental conditions.
Therefore, for the first time we can now in a cost-efficient manner make integrated use of this analysis capacity for developing a conceptual and methodological framework for the assessment of ecological status of the Baltic Sea ecosystem based on information on microbial functions and processes. Thus, this project will combine field studies, experiments, next-generation sequencing, bioinformatics and modeling to achieve the overarching objective: to establishing a capacity to reliably deduce Baltic Sea environmental status based on indicators reflecting the biodiversity and genetic functional profiles of microbes in seawater samples.
The Blueprint project has duration of 4 years (2014 - 2017), a budget of 3.9 million EURO, and is funded by the EU and the national research councils of Denmark, Sweden, Finland, Germany and Estonia. The project is coordinated by Prof. Lasse Riemann, University of Copenhagen.
Blueprint is funded by the BONUS programme through the European Community's Seventh Framework Programme (FP/2007-2013) under implementation agreement n R&I/I3/2012/BONUS made with BONUS, the joint Baltic Sea research and development programme.
University of Copenhagen, Denmark
KTH Royal Institute of Technology (KTH), Sweden
Stockholm University (SU), Sweden
Linnaeus University (LNU), Sweden
University of Helsinki (UH), Finland
Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Germany
University of Tartu (UT), Estonia
Scripps Institution of Oceanography, USA
University of California, Santa Cruz (UCSC), USA
The Blueprint project contains seven interacting work packages (WPs):
WP1 (Klaus Jürgens): Spatio-temporal variation of BLUEPRINTs (in situ data)
In this WP we aim to identify the linkage between different environmental conditions and the functional profile / diversity (the genetic blueprint) of microbes in the Baltic Sea. This will be done through extensive sampling of the fundamentally different subsystems of the Baltic, the abiotic gradients, and the seasonal variation.
WP2 (Veljo Kisand): Coupling of rates and genes
This WP aims at experimentally identifying key genetic and functional properties of natural microbial assemblages exposed to well-defined stressors which are known to constitute major environmental concerns in the Baltic Sea (e.g., hypoxia, N limitation leading to N2-fixing cyanobacterial blooms, and increased input of DOM/organic contaminants). The WP serves as an experimental examination of the links between environmental conditions and BLUEPRINTs identified in situ (WP1).
WP3 (Jarone Pinhassi): Identification of BLUEPRINTs in model bacteria
The objective of WP3 is to experimentally investigate responses in key diagnostic genes to selected external drivers/stressors. With this objective, we will carry out ecophysiological response experiments with genome-sequenced model bacteria and cyanobacteria to establish causal links between key environmental stressors and genetic signatures and selected nutrient fluxes/biogeochemical process rates of bacteria.
WP4 (Anders Andersson): Sample processing and statistical analysis (bioinformatics pipeline)
WP4 provides the bioinformatics infrastructure for extracting meaningful signals from the data collected in other WPs and for facilitating easy sharing of data across the WPs.
WP5 (Åke Hagström): Evaluation of genes and rates, design of reference experiments
Biogeochemical modeling is an essential tool to design management actions required to reach environmental targets set e.g. by HELCOM’s Baltic Sea Action Plan (BSAP) and the EU Marine Strategy Framework Directive (MSFD). It is therefore an essential task to generate additional scientific support for the formulation of Baltic biogeochemical models. The goals of WP5 are to a) use microbial blueprints to validate and improve parameterization of basin-scale biogeochemical models of the Baltic Sea. In particular, we will address key processes in biogeochemical cycling, e.g., carbon and nutrient mineralization, N2 fixation and denitrification, and b) provide an envelope covering a range of different environmental conditions, to optimize the sampling and experimental efforts in WP1 and WP2.
WP6 (Matthias Labrenz): BCC development and evaluation (standardization, communication)
The focus of WP6 is the transfer and integration of new microbial descriptors into existing monitoring procedures. Several aspects have to be considered, going deep into very different disciplines ranging from basic science over bioinformatics and potential development or adaptations of new instrumentations. WP6 will merge these aspects by improving, developing, evaluating, and standardizing general and specific working procedures to guide BLUEPRINT into practical operability within the virtual BLUEPRINT Competence Center (BCC).
WP7 (Lasse Riemann): Management and BCC dissemination
The objectives of this WP are to a) ensure efficient project management allowing for successful accomplishment of the described tasks and timely production of deliverables, and b) ensure dissemination of the project outcome to relevant institutions and policy makers.
Publications in press / published (peer-reviewed publications arising from the project research with authors from, at least, two different participating states)
- Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, et al. 2014. Binning metagenomic contigs by coverage and composition. Nature Methods 11, 1144-1146
- Logue JB, Stedmon CA, Kellerman AM, Nielsen NJ, Andersson AF, Laudon H, Lindström ES, Kritzberg ES. 2015. Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter. ISME J. 10: 533-545
- Teikari J, Österholm J, Kopf M, Battchikova N, Wahlsten M, Aro EM, Hess WR, Sivonen K. 2015. Transcriptomic and proteomic profiling of Anabaena sp. strain 90 under inorganic phosphorus stress. Appl Environ Microbiol 81:5212–5222.
- Hu Y, Karlson B, Charvet S, Andersson AF. Diversity of Pico-to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea. 2016. Front Microbiol.; 7: 679.
- Vaquer-Sunyer R, Reader HE, Muthusamy S, Lindh MV, Pinhassi J, Conley DJ, and Kritzberg ES. 2016. Effects of wastewater treatment plant effluent inputs on planktonic metabolic rates and microbial community composition in the Baltic Sea. Biogeosciences. 13:4751–4765. doi: 10.5194/bg-13-4751-2016
- Traving SJ, Rowe O, Jakobsen NM, Sørensen H, Dinasquet J, Stedmon CA, Andersson A, Riemann L. 2017. The effect of increased loads of dissolved organic matter on estuarine microbial community composition and function. Frontiers in Microbiology 8: 351
- Alneberg J, Sundh J, Bennke C, Beier S, Lundin D, Hugerth LW, Pinhassi J, Kisand V, Riemann L, Jürgens K, Labrenz M, Andersson AF. 2018. BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea. Scientific Data volume 5, Article number: 180146 (2018)
- Happel E, Bartl I, Voss M, Riemann L. Extensive nitrification and dominance of active bacterial ammonia oxidizers in two contrasting coastal systems of the Baltic Sea. 2018. In press, Environmental Microbiology
- Teikari JE, Hou S, Wahlsten M, Hess WR, Sivonen K. 2018. Comparative genomics of the Baltic Sea toxic cyanobacteria Nodularia spumigena UHCC 0039 and its response to varying salinity. Frontiers in Microbiology, 9: 356.
- Teikari JE, Fewer DP, Shrestha R, Hou S, Leikoski N, Mäkelä M, Simojoki A, Hess WR, Sivonen K. 2018. Strains of the toxic and bloom-forming Nodularia spumigena (cyanobacteria) can degrade methylphosphonate and release methane. ISME Journal, 12: 1619–1630.
- Markussen T, Happel EM, Teikari JE, Huchaiah V, Alneberg J, Andersson AF, Sivonen K, Riemann L, Mathias Middelboe M, Kisand V 2018. Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change. In press, Environmental Microbiology
Publications in press / published that acknowledge BONUS and BONUS BLUEPRINT (but do not have authors from at least two different participating states)
- Muthusamy S, Baltar F, González JM, and Pinhassi J. 2014. Dynamics of metabolic activities and gene expression in the Roseobacter clade bacterium Phaeobacter sp. MED193 during growth with thiosulfate. Applied and Environmental Microbiology. 80(22):6933-6942.
- Hugerth LW, Wefer HA, Lundin S, Jakobsson HE, Lindberg M, Rodin S, Engstrand L, Andersson AF. 2014. DegePrime, a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies. Applied and Environmental Microbiology 80(16):5116-5123.
- Hugerth LW, Muller EEL, Hu YOO, Lebrun LAM, Roume H, Lundin D, Wilmes P, Andersson AF. 2014. Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia. PLoS ONE 9(4): e95567.
- Lindh MV, Sjöstedt J, Andersson AF, Baltar F, Hugerth L, Lundin D, Muthusamy S, Legrand C, Pinhassi J. 2015. Disentangling seasonal bacterioplankton population dynamics by high frequency sampling. Environmental Microbiology. 17(7):2459–2476.
- Lindh MV, Figueroa D, Sjöstedt J, Baltar F, Lundin D, Andersson A, Legrand C, Pinhassi J. 2015. Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities. Frontiers in Microbiology. 6:Article 223
- Leisner JJ, Jørgensen NOG, Middelboe M. 2015. Predation and selection for antibiotic resistance in natural environments. Evolutionary Applications. doi:10.1111/eva.12353
- Hagström Å, Azam F, Berg C, and Zweifel UL. Culture the Marine Microbiome. Journal of Aquatic Microbial Ecology SPECIAL ISSUE 6: Progress and perspectives in aquatic microbial ecology: Highlights of the SAME 14 conference, Uppsala, Sweden, 2015. Editors: Paul A. del Giorgio, Fereidoun Rassoulzadegan, Eva Lindström. In press.
- Bunse C, Lundin D, Karlsson CMG, Akram N, Vila-Costa M, Palovaara J, Svensson L, Holmfeldt K, González JM, Calvo E, Pelejero C, Marrasé C, Dopson M, Gasol JM, Pinhassi J. 2016. Response of marine bacterioplankton pH homeostasis gene expression to elevated CO2. Nature Climate Change 6: 483-487
- Bombar D, Paerl R, Riemann L. 2016. Marine Non-Cyanobacterial Diazotrophs: Moving beyond Molecular Detection. Trends Microbiol. 24(11): 916-927. doi: 10.1016/j.tim.2016.07.002
- Lindh MV, Sjöstedt J, Casini M, Andersson A, Legrand C, and Pinhassi J. 2016. Local environmental conditions shape generalist but not specialist components of microbial metacommunities in the Baltic Sea. Frontiers in Microbiology. 7:Article 2078. doi: 10.3389/fmicb.2016.02078
- Traving SJ, Bentzon-Tilia M, Knudsen-Leerbeck H, Mantikci M, Hansen JLS, Stedmon CA, Sørensen H, Markager S and Riemann L. 2016. Coupling bacterioplankton populations and environment to community function in coastal temperate waters. Frontiers in Microbiology, 7: 1533
- Lindh MV, Sjöstedt J, Ekstam B, Casini M, Lundin D, Hugerth LW, Hue Y, Andersson AF, Andersson A, Legrand C, and Pinhassi J. 2017. Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers. Environmental Microbiology. In Press. DOI: 10.1111/1462-2920.13650
- Muthusamy, S., D. Lundin, R. M. M. Branca, F. Baltar, J. M. González, J. Lehtiö and J. Pinhassi. 2017. Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria. Environmental Microbiology. 19(6):2301–2319. doi:10.1111/1462-2920.13725
- Bunse, C. and J. Pinhassi. 2017. Marine bacterioplankton seasonal succession dynamics. Trends in Microbiology. 25(6):464-505. DOI: http://dx.doi.org/10.1016/j.tim.2016.12.013
- Beier, S., Shen, D., Schott, T., Jürgens, K. 2017. Metatranscriptomic data reveal the effect of different community properties on multifunctional redundancy. Molec. Ecol. 26: 6813-6826.
- Middelboe M, Brussaard CPD. 2017. Marine viruses: Key players in marine ecosystems. Viruses 9 (10), 302, 1-6. Doi: 10.3390/v9030049.
- Bennke, C. M., Pollehne, F., Müller, A., Hansen, R., Kreikemeyer, B., Labrenz, M. 2018. The distribution of phytoplankton in the Baltic Sea assessed by a prokaryotic 16S rRNA gene primer system. J Plankton Res, doi:10.1093/plankt/fby008.
- Shen, D., Jürgens, K., Beier, S. 2018. Experimental insights into the importance of ecologically dissimilar bacteria to community assembly along a salinity gradient. Environ. Microbiol. 20: 1170-1184.
- Paerl RW, Bertrand E, Rowland E, Scatt P, Mehiri M, Niehaus T, Hanson AD, Riemann L, Yves-Bouget F. 2018. Carboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis. Scientific Reports, 8: 5940
- Benavides M, Bonnet S, Berman-Frank I, Riemann L. 2018. Deep into oceanic N2 fixation. Frontiers in Marine Science, 5:108
- Paerl RW, Hansen T, Henriksen NNSE, Olesen AK, Riemann L. 2018. N-fixation and related O2 constraints on model marine diazotroph Pseudomonas stutzeri BAL361. Aquatic Microbial Ecology, 81: 125-136
- Bombar D, Paerl RW, Anderson R, Riemann L. 2018. Filtration via conventional GF/F -filters in 15N2 tracer assays fails to capture all nitrogen-fixing prokaryotes. Frontiers in Marine Science 5:6
- Shiozaki T, Bombar D, Riemann L, Sato M, Hashihama F, Kodama T, Tanita I, Takeda S, Saito H, Hamasaki K, Furuya K. 2018. Linkage between dinitrogen fixation and primary production in the oligotrophic South Pacific Ocean. Global Biogeochemical Cycles, in press