Stream Biofilm and Biogeochemistry Lab


Dept. of Limnology and Bio-Oceanography | University of Vienna

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Welcome to the Stream Biofilm and Biogeochemistry Lab!

We conduct basic research on the biogeochemistry of stream ecosystems and their microbial inhabitants, namely microbial biofilms. We combine experimental work and field surveys with ecological theory to gain mechanistic understanding of the coupled physical, chemical and biological processes that control the biogeochemistry of stream ecosystems.

Current and former projects address the following research:

  • Drivers of carbon dioxide evasion from Alpine stream networks
  • Microbial diversity and co-occurrence of biofilm communities in fluvial networks
  • Chemical source attribution and modification of terrestrial organic matter in streams
  • Architecture and morphogenesis of stream biofilms
  • Hyporheic exchange and biogeochemical hotspots in Alpine streams
  • Whole-ecosystem metabolism in fluvial networks

Our experimental facilities include various flumes and bioreactors, and field work comprises large-scale surveys and long-term monitoring of stream chemical and hydrological parameters. We are affiliated with the WasserCluster Lunz GmbH where we operate most of our experimental facilities. Learn more about our experimental facilities and field sites, as well as our team.




Recent Lab News:

2016-06: New Paper on Network-Scale CO2 evasion published

A paper on Network-scale CO2 evasion authored by Jakob Schelker and Co-Authors has been published in the journal Limnology and Oceanography.

Schelker, J., G. A. Singer, A. J. Ulseth, S. Hengsberger, and T. J. Battin (2016). CO2 evasion from a steep, high gradient stream network: importance of seasonal and diurnal variation in aquatic pCO2 and gas transfer. Limnol. Oceanogr. in press. doi:10.1002/lno.10339


2016-04: Karoline Wagner defending PhD Thesis

Karoline Wagner, PhD student at the lab, supervised by Tom Battin will be defending her PhD thesis with the title 'Are stream Biofilms prime sites for Priming'. Also, Prof. Anna Romani will be visiting us for this event.

The defense will be on Friday, 2016-04-22, at 11:00h in the Seminar Room Limnology.


2016-04: Dr. Manousos Valyrakis visiting the Lab

Dr. Manousos Valyrakis from the University of Glasgow, UK will be visiting our lab to give a talk entitled: 'Assessing the capacity of turbulent flows to conduct geomorphic work'.

The talk will take place at the Seminar Room Limnology on Thursday, 21th of April 2016 at 15h. 


2016-04: Strong presence at EGU conference

We are at the EGU meeting 2016! Kyle Boodoo will be presenting a poster on the thermal variability within the hyporheic zone of an Alpine stream gravel bar and Elisabet Ejarque will present a poster on the dual role of lakes as buffers and amplifiers of dissolved organic matter dynamics.


2016-03: Jakob Schelker to SFS Meeting in Sacramento

Jakob Schelker has been invited as a speaker to talk about forest disturbance and stream ecosystems at the Society for Freshwater Science - SFS Annual Conference in Sacramento, CA, USA in May 2016.


2016-03: Lukas Thuile Bistarelli sucessfully defends MSc Thesis

MSc Student Lukas Thuile Bistarelli has sucessfully defended his MSc thesis with the title 'The Effect of Soil Additions on DOM Dynamics and Biofilm Growth in stream Mesocosms'. Congratulations Lukas!


2016-02: Work on DOC leaching in boreal forests featured in EOS-Earth & Space Science News

Work on stream DOC dynamics under climate and land-use change done by a Swedish reasearch Team including Jakob Schelker has been featured in the EOS magazine. The original article on this work has been published in the journal JGR Biogeosciences.


2016-01: Kyle Boodoo and Jakob Schelker visit UFZ Leipzig

During this week, Kyle Boodoo and Jakob Schelker were in the city of Leipzig to meet with the other Interfaces project partners at the UFZ Leipzig, Germany. 


2015-11: Experimental Work on Streamside Flumes on Stream C-Cycling Featured in ORF 2 State TV Program

Our work at the Lunzer:::Rinnen was featured in a TV program aired on the ORF2 TV Channel on Suturday, 2015-11-2. Please visit the ORF website to watch the program (in German, availiable till 2015-12-11).


2015-10: Christina Fasching sucessfully defends PhD

Christina Fasching, PhD student at the lab has sucessfully defended her impressive PhD thesis. We wish you all the best Dr. Fasching!


2015-09: Katharina Besemer back at the Lab

After a one year study visit at the University of Glasgow, UK, Katharina Besemer has rejoined the Lab. Welcome back, Kathi!


2015-08: Kyle Boodoo Presenting his Research on Youtube

Kyle Boodoo, Interfaces PhD student at the lab is presenting his research together with the other Interfaces project fellows on Youtube. Have fun watching.


2015-08: Visitors for ongoing Flume Experiments

Astrid Harjung, interfaces PhD Student at the University of Barcelona and Nicolas Escoffier from EPFL are visiting the lab to collaborate on the ongoing flume experiments in the Lunzer Rinnen.


2015-07: New Project on Extreme Events featured in the Uni:View magazine

The EXCARB project is featured in the Uni:View Magazine that reports on ongoing work at the University of Vienna. Link to article (in german).


2015-06: Gordon Conference on Catchment Science

Jakob Schelker has been participating in the 2015 Gordon Conference on Catchment Science. What a great meeting!


2015-06: Upcoming PhD Defense!

Linda Wilhelm, PhD student at the Lab will defend her PhD thesis on the 18th of June, 11am.

We wish her all the best for this important step! Go Linda!


2015-05: Article on Mercury modeling in boreal streams published!

An article presenting a simple model for predicting mercury concentrations in small streams was published in ES&T.

Eklöf K, Kraus A, Futter M, Schelker J, Meili M, Boyer EW, Bishop K: A parsimonious model for simulating total mercury and methylmercury in boreal streams based on riparian flow paths and seasonality. Link to journal.


2015-04: Dr. Elisabet Ejarque Gonzalez joining the lab

Dr. Elisabet Ejarque Gonzalez, previously based at the University of Barcelona, Spain has joined our lab as a Post-Doc working on the EXCARB project. We wish her a warm welcome!


2015-04: Strong Presence at EGU and FBFW Meetings

At the EGU General Assembly, Jakob Schelker held an invited talk on CO2 evasion and Kyle Boodoo presented a poster. Also, Robert Niederdorfer and Lukas Thuile Bistarelli presented posters at the Fresh Blood for Fresh Water meeting in Mondsee, Austria. There, Lukas poster was ranked as the third best poster presentation - Congratulations!


2015-03: Amber Ulseth moving to EPFL Lausanne

Amber Ulseth is now moving from the University of Vienna to EPFL Lausanne. As our common work will continue, she will remain an integral part of our group. We wish her all the best for her new start in Switzerland!


2015-03: Guest Lecture by Andreas Hartmann, University of Freiburg, Germany

Andreas Hartmann from the University of Freiburg, Germany is visiting our lab and will be giving a guest lecture:

Title “Subsurface heterogeneity and water balance – lessons learned from modeling karst watersheds at different scales”

Wednesday, 11th of March 2015,  14:00h, Seminar Room Limnology


2015-03: Kyle Boodoo visiting UFZ Leipzig, Germany

Kyle Boodoo, PhD student at our lab will be visiting the Helmholtz Centre for Environmental Research - UFZ in Leipzig to work with the Fleckenstein Lab on modeling surface water - groundwater interactions. 


2015-02: Strong presence at the ASLO Aquatic Sciences Meeting, Granada, Spain

Yes, we are also going to the ASLO meeting in Granada! We will have a total of four presentations (please click for abstracts): Mia Bengtsson, Jakob Schelker, Amber Ulseth and Tom Battin. This will be great fun!


2015-01: Amber Ulseth is serving at a PhD Defense Comittee

Amber Ulseth is serving on a PhD Defense Comittee at the University of Barcelona, Spain.


2015-01: Jakob Schelker visiting the CRP Gabriel Lippmann, Luxembourg

Jakob Schelker is visiting the CRP Gabriel Lippmann in Luxembourg to give a seminar on nitrate cycling in boreal and lower alpine streams and to talk about other interesting science and visiting the field sites.


2014-11: Fieldwork at the large streamside flumes featured in WCL Newsletter

Our experiment performed this fall at the Lunzer:::Rinnen is featured in the Wassercluster Lunz Newsletter.

Download the Newsletter here (in German).


2014-11: Post-Doc position opening at WCL.

We are ready to hire a three-year post-doc working on hydrological extremes and carbon fluxes in aquatic ecosystems.

Interested? Take a look here.


2014-10: Upcoming talk by Dr. Emily Bernhardt from Duke University. 

Dr. Bernhardt will give a seminar entitled ‘Stream ecosystems in the urban wilderness: watershed degradation, river restoration and new frontiers for urban landscapes’.

Her talk will take place on Wednesday, 19 November 2014 at 12:00 in the Limnology seminar room (UZA I).

For more information on her work please visit: http://bernhardtlab.weebly.com


2014-10: New article on responses of biofilms to varying DOC sources published in 'Applied and Environmental Microbiology'!

A new article on the functional and structural responses of hyporheic biofilms to varying DOC sources by Karoline Wagner et al., has been published in the AEM Journal. Find out more here.


2014-10: Jakob visiting the Krycklan Symposium in Umeå, Sweden.

Jakob Schelker has been visiting the 11th Krycklan Symposium in Sweden. Read more on the Krycklan Symposium.


2014-09: Tom appointed Full Professor at EPFL!

Tom Battin got appointed Full Professor in Ecohydraulics at the Ecole Polytechnique Fédérale de Lausanne (Switzerland). He starts his new position in January next year, which means that some of us will travel between Vienna and Lausanne!


2014-08: Article on microbial Co-occurence in fluvial Networks published in PNAS!

Widder, S., et al., (2014): Fluvial network organization imprints on microbial co-occurrence networks, Proceedings of the National Academy of Sciences. Link to journal article.