Stream Biogeochemistry Lab

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

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The Stream Biogeochemistry Lab has moved!

Thank you for your interest in our research. As I am no longer associated with the University of Vienna, this website is no longer updated (2022-01).

Yours -  Dr. Jakob Schelker



Welcome to the Stream Biogeochemistry Lab!


Streams connect the terrestrial ecosystems with the global oceans. Our research concerns the biogeochemical transformations that take place along this journey. Specifically we try to understand the fundamental mechanisms of transport and biogeochemical cycling of solutes, such as carbon, nutrients and metals in fluvial ecosystems.

We are combining experimental work at different spatial scales with field surveys and process-based modelling approaches. Besides gaining scientific knowledge we also strive to apply our findings to evaluate risks for the functioning and health of stream ecosystems that originate from anthropogenic perturbations, such as climate and/or land-use change.

Current and former projects address the following research:

  • The impact of climate extremes on stream and lake organic matter turnover
  • Drivers of carbon dioxide evasion from Alpine streams
  • Hyporheic exchange and biogeochemical hotspots in Alpine streams
  • Chemical source attribution and aquatic modification of terrestrial organic matter
  • Controls on microbial diversity and functioning of stream biofilms

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 a part of the WasserCluster Lunz where we operate most of our experimental facilities. Learn more about our experimental facilities and field sites, as well as our team.


Dept. of Limnology &
Wasser Cluster Lunz








Recent Lab News:

2022-01: Paper on Bubble Mediated Gas Exchange in Turbulent Streams

The Paper "Unravelling the Contribution of Turbulence and Bubbles to Air-Water Gas Exchange in Running Waters"

by M. Klaus and Co-authors has been published in the Journal JGR-Biogeosciences.


2021-07: Paper on Eddy-Covariance methods at Lake Lunz out!

Atmospheric CO2 Exchange of a Small Mountain Lake: Limitations of Eddy Covariance and Boundary Layer Modeling Methods in Complex Terrain, by  K. Scholz, and Co-authors has been published in the Journal JGR-Biogeosciences.


2021-05: Paper on the Carbon Mass balance of Lake Lunz out!

yet another late paper originating from the ÖAW-ESS EXCARB project titled Hydrology controls the carbon mass balance of a mountain lake in the eastern European Alps has been published in the Journal Limnology&Oceanpgraphy.


2021-04: Paper on Drought Effects on Hyphoreic Carbon Processing published

A paper titled Experimental desiccation indicates high moisture content maintains hyporheic biofilm processes during drought in temperate intermittent streams
by Laura Coulson et al., has been published in the Journal Aquatic Sciences. Excellent work Laura!


2021-02: Paper on Chamber Methods published

A collaborative paper involving researchers from Italy, France, Sweden and Austria from the AQUACOSM-TA Experiment held in Lunz am See, Austria was sucessfully published:  Evaluating stream CO2 outgassing via drifting and anchored flux chambers in a controlled flume experiment by Filippo Vingiani and Co-authors in Biogeosciences.


2021-01: Paper on Soil Microbial Inoculation of Stream Ecosystems out!

Our first one to explicitly show that high-flows are important to shape stream microbial communities through soil microbial inoculation: Soil microbial inoculation during flood events shapes headwater stream microbial communities and diversity by Florian Caillon, Katharina Besemer, Peter Peduzzi and Jakob Schelker was published in Microbial Ecology.


2020-10: Paper on FM-4 Frequency Music Festival attracted large Media attention

Our paper published in ES&T in August 2020 on the Festival impact attracted widespread media attention by Austrian Newspapers (mostly in German), online-news outlets and national radio stations:

  8. A two piece Radio Interview on the results were broadcast on the FM-4 Station in English on 27/08/2020.


2020-08: Paper on the Impact of the FM-4 Frequency Music Festival Published


Our new paper titled 'High anthropogenic organic matter inputs during a festival increase river heterotrophy and refractory carbon load' is out in ES&T.

Link to article (Open Access):

Good work everyone - Reading is highly recommended!


2020-04: Kyle Boodoo successfully defends PhD Thesis

Kyle Boodoo, PhD candidate within the group has successfully defended his PhD thesis titled: "The Role of Gravel Bars in Stream Reach Scale Carbon Biogeochemistry".

Good work and congratulations Dr. Boodoo!


2020-03: Paper on Soil-Stream Transfer of Microbes Published

A paper  titled "Dynamic transfer of soil bacteria and dissolved organic carbon into small streams during hydrological events" by Florian Caillon and Jakob Schelker was published in Aquatic Sciences.

Read the paper here


2019-11: Newsletter of WCL is out

The current Newletter by the WasserCluster Lunz (in German) features an editorial, as well as an article about our recent work.

Read more here.


2019-09: Sucessfull Flume Experiment on Stream Gas exchange in Lunz

As part of the AQUACOSM Transnational Access, we hosted a flume experiment with Marcus Klaus (SWE), Gianluca Botter (ITA), Thierry Labasque (FRA) and David Vilbert (FRA) at our flume facilities in Lunz. Read more here and here

Thanks for a great experiment!


2019-07: Florian Caillon presenting at SEFS in Zagreb

Caillon et al.,: Hydrological events mobilize dissolved organic carbon and soil microbes into small streams.

11th Symposium for European Freshwater Sciences, June 30–July 5, 2019, Zagreb, Croatia


2019-05: Paper on Modelling Stream Gravel-Bar CO2 evasion published

K.S. Boodoo, J. Schelker, N.Trauth, T.J. Battin and C. Schmidt: Sources and variability of CO2 in a preā€alpine stream gravel bar

Good work Kyle!


2019-02: Strong presence at EGU General Assembly

The group will give two oral presentations at the EGU General Assembly 2019:

Schelker et al., on soil microbial inoculation of streams

Harjung et al., on synthetic DOM sources streams.

Hope to see you at EGU in April!  


2018-10: Astrid Harjung visiting WOMS workshop in France!

Astrid Harjung presented our work on soil DOM from the HYDRO-DIVERSITY project at the International Workshop on Organic Matter Spectroscopy 2018 in La Garde City, France – Organized by Université de Toulon and Aix-Marseille Université


2018-08: Paper on Drought Effects on DOM Dynamics in Streams published!

A wonderful paper on DOM dynamics during an actificially created drought by Astrid Harjung and Co-authors has been published online in L&O. Congratulations Astrid!


2018-07: Opportunity for field Experiment

Do you have a good idea for a controlled experiment in streamside flumes? If so, continue reading here!


2018-06: Soil Runoff Samplers (SRS) fully operational

Our new field sites, the Soil Runoff Samplers (SRS) are now fully operational and have just measured the first big storm event of this summer for the HYDRO-DIVERSITY project. Thanks to Mike, Hannes, Florian and all the other helping hands for setting them up!


2018-05: Astrid Harjung has joined the team

Astrid Harjung, previously at the Univeristy of Barcelona has joined our team as a Post-Doc researcher. She will be working in the HYDRO-DIVERSITY project.

Welcome Astrid!


2018-04: Opportunity for Collaboration

Come work with us on our Experimental Flumes! Apply for travel and analysis support; the next call will open shortly:


2018-04: Strong presence at EGU Meeting 2018

we are present at the EGU meeting 2018 with the following presentations: Boodoo et al.,; Schelker et al.,

2018-02: Newspaper Article in 'Der Standard'

An article describing our work on streams and climate change has been published in the 'Science Special' section of the daily newspaper 'Der Standard'. Read the full Article here (in German)!

2018-02: Florian Caillon joining the Group

Florian Caillon has joined our team as a PhD-Student to study microbes. Welcome Florian - may the microbes be with you!

2018-01: Paper on Lake DOM transformation published in L&O

a wonderful new paper on the shifting role of lakes with climate change has been published. Congratulations Elisabet!

Ejarque, E., S. Khan, G. Steniczka, J. Schelker, M. J. Kainz and T. J. Battin "Climate-induced hydrological variation controls the transformation of dissolved organic matter in a subalpine lake." Limnology and Oceanography DOI: 10.1002/lno.10777

2017-12: PhD Position availiable

We are opening another 3-year PhD position on on Flow Intermittency on Hyporheic Biogeochemistry in collaboration with Dr. Gabriele Weigelhofer. Application deadline is December 31st, 2017. The position will be based at WasserCluster Lunz.

2017-10: Paper Published in Scientific Reports

A wonderful paper demonstrating the relevance of gravel bars in stream corridors as sources of atmospheric CO2 has been published by Kyle Boodoo - Congratulations Kyle!

Ref: Boodoo, K. S., N. Trauth, C. Schmidt, J. Schelker and T. J. Battin (2017). "Gravel bars are sites of increased CO2 outgassing in stream corridors." Scientific Reports 7(1): 14401.

2017-08: PhD Position availiable

We are opening a 3-year PhD position on Microbial Ecology of Stream Biofilms within the new project HYDRO-DIVERSITY. Application deadline is September 30th, 2017. The position will be based at WasserCluster Lunz.

2017-06: Gordon Conference on Catchment Science about to take off!

The Gordon Research Conference on Catchment Science chaired by Dr. Kevin McGuire (Virginia Tech) and Jakob Schelker with the title 'Crossing Boundaries and Seeking Synthesis in the Catchment Sciences' is about to take off.

Looking forward to discussions at the forfront of our field and to meet many collegues and friends.

2017-05: Paper in WRR published

A group paper on the role of interfaces in catchment biogeochemistry by Stefan Krause et al., has been published in Water Resources Research.

Krause, S., J. Lewandowski, N.B. Grimm [...]: Ecohydrological interfaces as hotspots of ecosystem processes. Water Res. Research. doi/10.1002/2016WR019516

2017-04: Paper in Ecosystems published

A paper by Amber Ulseth on the impact of climate change on snowmelt and the implications for network-scale stream metabolism published in ecosystems.

Ulseth, A.J., E. Bertuzzo, G.A. Singer, J. Schelker, and T.J. Battin: Climate-Induced Changes in Spring Snowmelt Impact Ecosystem Metabolism and Carbon Fluxes in an Alpine Stream Network. Ecosystems. doi:10.1007/s10021-017-0155-7

2017-01: Jakob Schelker on Parental Leave

Science is important, but other things are too. Thus, Jakob Schelker has been on leave with his one year old son from Sept. 2016 to Jan. 2017.

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:

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.