Nordic Environmental NUcleotide Network

News about NENUN

8th NENUN Workshop (14-16 November 2017)

June 11th, 2017

The 8th Nenun Workshop will take place on 14- 16 November 2017 at Copenhagen Bio Science Park (COBIS).


Please register and/or submit your abstract HERE

Registration fees
Participant: 800DKK

Social events
Dinner at COBIS (14.11.2017): Free of fee – registration is required
Walking Tour at Assistens Kirkegård: Free of fee – registration is required
Dinner at Bodega (15.11.2017): 250DKK (incl. 25% VAT)

Included in the registration fee
Admission to the full conference programme, final programme, coffee breaks and lunch, Dinner at COBIS (14.11.2017) and the walking tour at Assistens Kirkegård (15.11.2017).

Cancellation terms NENUN 2017
All cancellations must be notified in writing to the NENUN 2017 Secretariat:
Cancellations received on or before 16 October 2017 will incur a cancellation fee of DKK 150.
Cancellations after 16 October 2017 are non-refundable.

If, for reasons beyond the control of the organiser, the conference is cancelled the fees will be refunded after expenses incurred by the meeting have been deducted.






Workshop in Tromsø June 1-3 2015

December 16th, 2014

Workshop in Tromsø June 1-3 2015

Phd course Amplicon based microbial community

December 10th, 2014

Program Amplicon based microbial community course

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

Program for 4th NENUN workshop Uppsala

February 7th, 2013

Nenun Workshop Uppsala 2013

Read the rest of this entry »

3rd Network Workshop – Copenhagen Denmark 2012

February 4th, 2013

We had a successful workshop at the day off at ISME 2012 with around 100 participants and some really good talks. The topic of the day was Extraction of microbial DNA & RNA in environmental samples. The program can be seen here.

The NENUN network would like thank all the presenters and the participants for a very interesting day.


2nd Workshop Reykjavik 2011 – Resume

September 22nd, 2011


Travel grant

Up till now there have been no applications for travel grant from Nenun. Therefore it was decided that it should be more clear how to apply and an application document on the Nenun homepage. This should been done before 1st of October.

There will still be 4 deadlines for applications:

-          March 1st

-          June 1st

-          September 1st

-          December 1st

All applications should be send to, and cc to the host and own supervisor or group leader. It is expected that each person receiving funding will prepare a one page description of the stay or give a presentation on the forthcoming NENUN workshop.

The Nenun network will aim at paying for 5 exchanges a year of maximum 20.000 Norwegian kroner, and bench fee is not included. The funding will cover travel expenses and accommodation.

Ph.D. Courses

It was decided that Nenun network members will apply for two Ph.D. courses when it is possible from Nordforsk.

1st course – Ecological theory linked to microbial ecology:

It was not decided who should take the lead for this course. It was decided that either Anne Winding, Alexander Eiler or Sarah Hallin should take the responsibility for the course. This should be decided before 1st of October.

The course will take place in the connection with the next Nenun workshop in Upssala.

2nd course – Environmental Transcript Analysis and Transcriptomics:

It was decided that Carsten Suhr Jacobsen will take responsibility for the course. The following persons will be a part of the course:

-          Mette Haubjerg Nicolaisen

-          Jacob Bælum

-          Stefan Bertilsson

-          Binbin Liu

-          Åsa Frostegård



It was decided that there should be a disclaimer on the protocol page.

All agreed to submit the protocols to the Nenun secretary before 1st of October.

Isme Roundtable

It was decided that Nenun will apply for a roundtable at ISME next year. The application round will take place next year around March/April. The roundtable should be open and about DNA/RNA extraction. Carsten Suhr Jacobsen agreed to conduct a description of a roundtable and send it to the steering group. The steering group will then decided on the formulation of the roundtable application.

ISME Mixer

Mette Haubjerg Nicolaisen agreed to plan a Nenun mixer at ISME 2012. Mette will investigate whether it is Monday or Tuesday that will be best suitable. This will be held at the garden café at LIFE faculty at Copenhagen University.

Uppsala Workshop 2012

The next Nenun workshop will take place in Uppsala in October 2012. It was decided that the main focus on the workshop should be on methods.
Alexander Eiler, together with Morten, will plan the next workshop.

Convention on Biological Diversity

Preben Nielsen presented the Rio convention regarding the sampling permission in different countries.

All the information can be fund at –

For sampling permission for Greenland:

Steering group meeting 16th Marts

April 7th, 2011

Steering group meeting 16th Marts 2011 from 12.30 – 18

Attending at the meeting: Kim Yrjälä (Finland), Åsa Frostegård (Norway), Sara Hallin (Sweden), Andreas Schramm (Denmark), Solveig K. Pétursdóttir (Iceland), Morten Schostag Nielsen (Secretary), Carsten Suhr Jacobsen (Network leader)


1) The role of the steering group

2) Update on planning of PhD courses in NENUN

3) Update on new application and activities within the network

4) Agenda for next workshop in Reykjavik in September

5) Student-exchange

6) NENUN-methods

7) Homepage

8 ) Any other business

1) The role of the steering groups

It is the steering group’s role to support the activities in NENUN. The steering group will secure that the decisions from the NENUN workshops is implemented. The steering group will decide on support from NENUN to activities in the network including student exchange and research visit applications.

The steering group decided to meet just before the start of next NENUN workshop in Reykjavik Wednesday 7th September 2011 in the afternoon. After Reykjavik workshop it will be decided whether there should be another steering group meeting in February 2012.

2) Update on planning of PhD courses in NENUN

Andreas Schramm presented the plans for the course on Single cell methods. This course will be held 15th-21st of August in Sweden. Stefan Bertilsson will send out information on this later. The course will be posted on the homepage as soon as the description is ready.

The course “Ecological theory linked to microbial ecology” was originally planed to be applied for as a full NordForsk Research Training Course PhD course but is has now been decided that it can be supported as a NENUN course. It is expected to run in May 2012. Alexander Eiler and Sara Hallin are the responsible persons.

The other planned application for a full NordForsk Research Training Course “Environmental Transcript Analysis and Transcriptomics” has not been applied for in 2011 but will be applied for in 2012 and Carsten Suhr Jacobsen is the responsible person.

The application “ NGS data Ph.D. course “ by Marja Tiirola has been submitted to NordForsk for a full NordForsk Research Training Course with the inclusion of particular interested NENUN partners.

3) Update on new application and activities within the network

It was decided that the steering group will initiate the lobby work for a Nordic Centre of Excellence (NCoE) should start as soon as possible. Carsten will make a draft paper on the need for a Center of excellence in Microbial Ecology with specific implications for the Nordic aspect and Åsa Frostegård and Andreas Schramm will comment on this prior to involvement of the rest of the NENUN NCoE group. Sara volunteered to make contact to NordForsk to “dig out” their possible plans for the next NCoE .

4) Agenda for next workshop in Reykjavik in September

There was an agreement on four sessions at the workshop in Reykjavik. The four sessions will be as follows:

Session 1: Analysis of single cells and specific populations

This session covers single cell and population analyses in the environment, on all levels from the detection of genes or transcripts inside single microbial cells to the analysis of activity (substrate uptake) at the single cell level (e.g. MAR-FISH, nanoSIMS), to capturing single cells for gene or genome sequencing, and also includes the quantitative analysis of specific populations (e.g. by qPCR or FISH).

Session 2: Active microbes in the environment

This session covers the analysis of microbial communities in the environment that are performing specific activities. This could be quantitative analysis of functional genes (examples nitrogen related or pesticide related) or it could be measurement of microbial mediated biochemical processes. The use of sequencing analysis of transcripts – transcriptomics – to reveal new microbial pathways directly in environmental samples is also included.

Session 3: Functional diversity of microorganisms in different ecosystems

This session covers functional genes important for key functions of pristine ecosystems, but also functional gene diversity in response to environmental stress like pollutants or draught and other stressors. Functional gene diversity for discovering functions or changes in function of different ecosystems.

Session 4: Making ecological sense out of sequence data

This session deals with various ways to analyze sequence data to get insights into microbial ecology

There will be a three hour excursion Friday after noon. Destination has not be decided, Solveig will investigate were to go.

There is a maximum of 50 participants for Reykjavik. NENUN will pay for the stay for 2 persons per group.

Titles should be submitted to NENUN secretary before 1st of August.

5) Student-Exchange

It was decided that the network will aim at paying for 5 exchanges a year of maximum 20.000 Norwegian kroner. Funding will cover travel expenses and accommodation. Bench fee is not included. There will still be 4 deadlines for applications (March 1st, June 1st, September 1st, and December 1st). It was decided that not only PhD students but also post Doc’s and senior scientist can apply for this. Individuals can only receive funding once, but institutes may have several individuals who may receive funding.

All applications should be send to, and cc to the host and own supervisor or group leader. It is expected that each person receiving funding will prepare a one page description of the stay or give a presentation on the forthcoming NENUN workshop

The steering group will make an application form to be filled out. Applications should contain a template to be filled out, a full budget of the stay and a one page presentation of the project and reason for the stay.  The steering group will make a guideline for an exchange visits Carsten will make a draft and send to the steering group. After receiving the applications at the travel grant email address the NENUN secretary will send all applications to the members of the steering group. Each member ranks the applications from their own judgment and returns a prioritised list to the NENUN secretary within 14 days.

The steering group discussed the evaluation criteria of the judgement and it was decided that longer stays are preferable to secure real collaborative effect, but in certain cases also a short visit can be relevant.

The support is paid from GEUS to the host institution for the person travelling. The support will be paid after the trip, upon receiving 1) a one page description of the activities and 2) a bill from the host institution send to GEUS.

6) NENUN-methods

Carsten will make some example of what is expected of a protocol. This will be uploaded on the homepage.

7) Homepage

There was an agreement, that there should be a Job page on the home page for the network to post job positions. Contact Morten

8 ) Any Other business


Short resume of the decisions at the first NENUN workshop:

December 2nd, 2010

1. Next workshop? Price?

It has been decided that the next NENUN workshop will be held in Iceland. The meeting will take place in September 2011, date to be announced later.

The travel expenses for future workshop cannot be finance by NENUN. Accommodation and food etc. will be finance by NENUN for to persons per group.  NENUN workshop 2012 will take place in Uppsala.

2. Theme for next NENUN Workshop

For next NENUN workshop there will be a focus on specific subject sessions with reference to the possible work packages defined by the Centre of Excellence. The precise schedule for the next workshop will be defined by the board.

3. NENUN Methods

The list made on the flip board will be transformed to a separate page on the homepage. From this page each mark will open a new page by clicking and a 2-5 line descriptive text will appear (some groups might have more then one protocol).

- NENUN will not make quality control on these protocols so people themselves are responsible for the contents.

- Comment at the start of the protocol. Information about how good they are at these methods.

4. Short PhD students mission

- Exchange of PhD student can be applied by NENUN participants and the board will read the application and make judgedment on the amount of funding. 4 deadlines a year:  March 1th, June 1th; September 1th, December 1th

The applicants are asked to also consider national funds and FEMS stipends.

5. New Members

It was decided that the network cannot finance new members. However new members are welcome to apply for membership, but have to pay the cost of their own stay.

6. Sub groups.

It was decided to form a subgroup working on creating possibilities to apply for Center of Excellence (CoE) from NordForsk.

-          Sara Hallin

-          Søren J. Sørensen

-          Stefan Bertilsson

-          Andreas Schramm

-          Åsa Frostegård

-          Anne Winding

-          Kirsten Jørgensen

-          Lasse Riemann

7. NENUN PhD courses

NENUN will give seed money for up to three Ph.d. courses The seed money is maximum 30.000 norske kroner and implices a size of 10-15 student (NENUN student in favour)

- Stefan and Andreas takes lead on a course on Single cell methods

- Søren takes lead on a 454 sequencing (Søren) Stefan contribute with some people.

8. Norfa Ph.D. courses

It was agreed that the network will try to apply for one or two Ph.D. courses next time there is a possibility from NordForsk

-          Ecological theory linked to microbial ecology– Anne Winding, Mette Marianne Svenning, Kim Yrjälä, Sara Hallin, Alexander Eiler

-          Environmental Transcript Analysis and Transcriptomics – Carsten Suhr Jacobsen et al.

9. Steering group

- Finland: Kim Yrjälä

- Island: Solveig Petursdottir

- Sweden: Sara Hallin

- Norway: Åsa Frostegård

- Denmark: Andreas Schramm and Carsten Suhr Jacobsen

10. ISME Satellite

- Roundtale NENUN – The board applies

- Social mixer held with food and drink either Monday or Tuesday evening in a NENUN lab in Copenhagen

Network Meeting 23.-25. November

November 21st, 2010

A kick off meeting for the network taking place 23-25 November 2010 to facilitate further detailed planning and coordination of the activities in the network with the following agenda:

Tuesday November 23

12.00-13.00 Lunch
13.00-13.45 Introduction to NENUN – funding, rules, possibilities and requirements
13.45-14.00 Break
14.00-17.45 Group presentation
14.00-14.15 Arctic microbial ecology group at the Department of Arctic and Marine Biology, University of Tromsø. By Mette Marianne Svenning and Alexander Tveit
14.30-14.45 The molecular microbial ecology group at the Marine Biological Laboratory, University of Copenhagen. By Lasse Riemann
14.15-14.30 The Molecular Environmental Microbiology group, Department of Biosciences at the University of Helsinki. By Kim Yrjälä and Timo Sipilä
14.45-15.00 Break
15.00-15.15 Finnish Environment Institute. By Kirsten Jørgensen and Pirjo Anneli Yli-Hemminki
15.15-15.30 Microbial Ecology group, Department of microbiology at the Swedish University of Agricultural Sciences in Uppsala. By Sara Hallin and Allana Welsh
15.30-15.45 Geomicrobiology group at Department of Biology, Centre for Geobiology, University of Bergen. By Lise Øvreås and Vigdis Lid Torsvik
15.45-16-00 Break
16.00-16.15 Section of Microbiology at the Department of Environmental Chemistry and Microbiology, National Environmental Research Institute, Aarhus University. By Anne Winding and Tina Santl Temkiv
16.15-16.30 The  Freshwater Microbial Ecology group at the Department of Ecology & Evolution, Uppsala University. By Stefan Bertilsson and Alexander Eiler
16.30-16.45 The microbial biotechnology group at Department of Agriculture and Ecology, University of Copenhagen. By Peter Stougaard and Mette Haubjerg Nicolaisen
16.45-17-00 Break
17.00-17.15 Matis at the University of Iceland. By Snædis H. Björnsdottir and Solveig K. Petursdottir
17.15-17.30 Department of Environmental Engineering , DTU Environment at the Technical University of Denmark. By Barth F. Smets
17.30-17.45 Novozymes. By Preben Nielsen
17.45-19.00 Break
19.00–21.00 Dinner

Wednesday November 24

8.00-9.00 Breakfast and walk in the park
9.00-11.45 Group presentation
9.00-9.15 The UMB Nitrogen group at the Norwegian University of Life Sciences. By Åse Frostegård and Linda Bergaust
9.15-9.30 Department of Geochemistry at the Geological Survey of Denmark and Greenland. By Carsten Suhr Jacobsen
9.30-9.45 Department of Biological and Environmental Science at the University of Jyväskylä. By Marja Tiirola
9.45-10.00 Break
10.00-10.15 Plant-Microbe Interaction and Microbial Biodiversity group at the Department of Food and Environmental Sciences at the University of Helsinki. By Kaisa Wallenius And Anu Mikkonen
10.15-10.30 Molecular and medical microbial ecology group at Department of Clinical and Experimental Medicine, Division of Medical Microbiology at Linköping University. By Per-Eric Lindgren and Pontus Lindblom
1030-10.45 The Molecular Microbial Ecology group at the Department of Biological Sciences, Microbiology at Aarhus University. By Andreas Schramm
10.45-11.00 Break
11.00-11.15 The Center for Geomicrobiology, Department of Biological Sciences, Aarhus University. By Mark Lever and Beth Orcutt
11.15-11.30 The Molecular Microbiology and Ecology group at University of Copenhagen. By Søren Sørensen og Lars Hansen
11.30-11.45 The Department of Biotechnology, Chemistry and Environmental Engineering at Aalborg University. By Jeppe Lund Nielsen
12.00-13.00 Lunch
13.00-15.00 Workshop on priority of activities in NENUN 

The funding and possibilities – 5 ideas as preparation for group discussions (by Carsten Suhr Jacobsen) 20 minutes – Group discussions in 50 minutes 6 groups of 7-8 – plenum presentations of 5 minutes followed by discussion.

15.00-18.00 Continued discussion during excursion to Kronborg (we have rented Kronborg Castle after dark and will get an exclusive tour in this impressive monument from the time when the Danes ruled :) )
19.00-21.00 Dinner

Thursday November 25

8.00-9.00 Breakfast
9.00-11.00 4 inspirational talks on future use of molecular techniques in microbial ecology. 

Stefan Bertilsson (confirmed); Andreas Schramm (confirmed); nn and nn

11.00-12.00 Summary of workshop, future activities in NENUN, do we need a board?
12.00-13.00 Lunch for those who want (Optional)

Geological Survey of Denmark and Greenland - Øster Voldgade 10 - DK 1350 Copenhagen K - Denmark - Web: - Contact