Nordic Environmental NUcleotide Network

Program NENUN workshop, Helsinki 12th – 14th May 2014

August 29th, 2014

Program NENUN workshop, Helsinki 12th – 14th May 2014

The venue is Biocenter 3, Viikinkaari 1, Room 2402, ‘Telkän pönttö’


Monday May 12th

Registration and packed lunch 12-13.00

13.00 Opening of NENUN meeting 2014 by Kirsten and Kim

13.15 Carsten Suhr Jacobsen: Former and future activities in NENUN

Functional genes – hydrocarbons and biodegradation

13.30: Kirsten Jørgensen (Finnish Environment Institute): PAH degradation and PAH-ring hydroxylating dioxygenase (PAH-RHDα) genes in soils and sediments

13.50: Louise Feld (GEUS): Detection and quantification of degradation genes for phenoxyacid pesticides

14.10: Sajan Raju (University of Helsinki): Catabolic potential of alphaproteobacteria from the genome perspective

14.30: Aura Nousiainen (Finnish Environmental Institute): Radioisotope methods in expression studies of atrazine degradation

14.50-15.15 CAMPUS WALK and coffee break

15.15-16.15:  Olivia Mason (Florida State University, USA): Microbial response to the Deepwater Horizon oil spill


16.15-16.30 CAMPUS WALK back to own meeting room.


16.30: Antje Gittel (Århus University): Anaerobic oxidation of short-chain hydrocarbons in marine sediments: identification of microbial key players by functional gene assays and their application in oil & gas exploration

16.50: Mette Haubjerg Nicolaisen (University of Copenhagen) Significance of environmental stress for catabolic gene expression

16.50 – 17.00 Wrap of the afternoons program – : Kim Yrjälä

17.00. – 18.15 get-together at the University

Possibility for Sauna at the Finnish Environment Institute close to the hotel.

Tuesday May 13th

9.00 Announcements by Kim and Kirsten

Methods in functional gene analysis

9.15 Jacob Bælum (DTU) Methods for studying functional genes in microbial communities – from qPCR to shot gun sequencing

9.50 Natalie Lim (Norwegian University of Life sciences) The order of downstream enzymatic processes strongly affects the quality of soil-extracted nucleic acids used for metagenomics and metatranscriptomics analyses

10.10 Manu Tamminen (University of Helsinki) Making genomics small: single genome barcoding and targeted sequencing

10.30 – 11.00 coffee break

11.00: Stefan Bertilsson (Uppsala University): Single cell genomics in environmental microbiology

11.20: Alexander Eiler  (Uppsala University): GEFES: Pipeline for metagenomic assembly and annotation

11.40:  Wrap up of the mornings program – Kasper Kjeldsen

Lunch at noon, 12.00 In Gardenia restaurant (

13.15 – 13.50 . Kim Yrjälä (University of Helsionki): Functional genes and phylogeny, who are the hosts or are they just ghosts?


Functional genes – inorganic geochemistry

13.50 Vaibhav Diwan  (DTU): Functional gene approach to study nitrifier diversity

14.10 Jaak Truu (University of Tartu): Microbial community structure and abundance of  functional genes related to nitrogen transformation processes in different treatment wetlands

14.30 Kasper Urup Kjeldsen (University of Århus): Dissimilatory bisulfite reductase (dsrAB) as a functional marker gene for sulfate-reducing microorganisms

14.50 – 15.00 coffee break

15.00: Christopher Jones  (Swedish University of Agricultural Sciences): Biodiversity and N2O emissions – a functional gene perspective

15.20: Yun-Feng Duan (Kevin) (University of Århus): Community of denitrifying bacteria and nitrous oxide emissions in Danish grassland soils

15.40: Mette Marianne Svenning (Tromsø University): Methane oxidising bacteria in Arctic and Sub-Arctic peatlands

16.00: Marja Tiirola  (University of Jyväskylä): Functional analysis of uncultivated microbes using radioisotope probing  new ERC project “Micro-RIP”

16.20 Wrap of the afternoons program – Åsa Frostegaard

End of second day around 16.30

 Evening dinner on Suomenlinna fortress island

Departure ca. 18.30 from the Kauppatori  (market place) harbor


Wednesday May 14th

Start at 9 am

9.15 Oliver Muller (University of Bergen) Microbial communities in arctic environments ? Combining molecular methods and carbon flux analysis to study the impact of changes on biogeochemical processes


9.35: Windi Muziasari  (University of Helsinki): Distribution of Antibiotic Resistance Genes in Baltic Sea sediments using qPCR array


9.55: Ole Nybroe (University of Copenhagen) Development of bioreporters in P. putida mt-2 to study oxidative stress responses

10. 15 Discussion about making use of current network for applications (Norden, Horizon 2020, Cost, other EU funds). Discussions in smaller groups.

12.00 Ending of meeting and packed lunch

12.00-13.30 Steering group meeting

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