Recent Research Projects

Analysis and Control of Microbial Systems

Recent Research Projects



  • Evaluating the effects of different organic matter loads on microbial community dynamics in recirculating aquaculture systems (RAS) (2016-2019)
  • Host-microbe interactions in Atlantic cod larvae (2014-2019).
  • MicStaTech - Water treatment technology for microbial stabilization in landbased aquaculture systems (2015-2018)
  • MIRA – MIcrobially produced Raw materials for Aquafeed (2014-2018)
  • Gnotobiotic cod larvae to unravel microbe-microbe and microbe-host interactions (2014-2016)
  • Lipid production and photosynthesis in the microalga Nannochloropsis oceanica (2013-2016)
  • Aerobic and anaerobic oxidation at high salinities (2012-2016)
  • Biological N removal from process waste water of a CO2 capture plant (2008-2016)
  • BIONA - Biogas Reactor Technology for Norwegian Agriculture (2011-2014)
  • SOLBIOPTA - Biotechnological Production of Materials for Optimized Solar Cell Efficiency (2010-2013)Promicrobe - Microbes as positive actors for more sustainable aquaculture (2009-2013)
  • NSTTT – Norwegian Seaweed Technology Center (2012 – 2012)
  • Biorefinery Application (2011-2011)
  • Biogas Trøndelag - Microbial methods for design and operation of local biogas facilities (2009-2010)
  • Lipido - Optimizing Lipid Production by Planktonic Algae (2007-2011)
  • Ballast water – Evaluation of methods for treatment of microbes in ballast water (2005-2009)
  • CODTECH - A process oriented approach to intensive production of marine juveniles with main emphasis on cod (2003-2008)


Evaluating the effects of different organic matter loads on microbial community dynamics in recirculating aquaculture systems (RAS) (2016-2019)

A key challenge in recirculating aquaculture systems (RAS) is the accumulation of particulate organic matter. This can stimulate growth of bacteria as the supply of organic matter is typically the limiting resource determining the carrying capacity of heterotrophic bacteria in the system. An environment with rapid escalation of bacterial numbers, and frequent fluctuations in the microbial community dynamics could reflect an environment rich in opportunistic unfavorable bacteria. The overall aim for the project is to understand more about how organic matter in RAS affects the microbial community dynamics, and if there are operational strategies in RAS that could be more beneficial for the microbial water quality. An experiment to compare two RAS, with and without membrane filtration with resulting different organic matter loads, was conducted at the NTNU Sealab with Atlantic salmon parr. Analyses of Illumina sequencing, flow cytometry, Thymidine incorporation assay and general water quality were performed.

The project is in collaboration with Sintef, and the work is funded by the ERA-NET COFASP and the Norwegian Research Council project “Water treatment technology for recirculating aquaculture systems to increase efficiency by reducing the negative effects of organic matter (RAS-ORGMAT)” (260872/E40).

One PhD candidate and two master students work in this project.


Host-microbe interactions in Atlantic cod larvae (2014-2019).

The roles of host associated microbiota have been given increasingly more attention during the last decades. We know that bacteria are important (in several aspects regarding) for development, immunity and nutrition uptake of the host. However, for fish little is known about what determines the structure of the host associated microbial communities and how this affects the fish. In this project we are investigating how the microbial communities associated with cod at early life stages are influenced by the microbial communities in the environments, and how (the) they (evt. the microbiota) affect the cod. For this we use both experimental (size) aquaculture systems(,) and gnotobiotic husbandry.

One PHD candidate Ragnhild Inderberg Vestrum is financed by Faculty scholarship.


MicStaTech - Water treatment technology for microbial stabilization in landbased aquaculture systems (2015-2018)

The paradigm of this project is that a stable, elevated microbial abundance in the water phase of land based aquaculture systems can be beneficial for fish health and economically profitable. A common challenge in land based systems, and shown across species, is the loss of fish due to unfavourable conditions and disease outbreaks that may be linked to opportunistic bacteria. A popular approach to prevent this is to attempt to reduce the load of bacteria in the systems by the use of UV or ozone disinfection. This is however not possible or sufficient in the majority of systems, because disinfection has a non-lasting effect on the numbers and a destabilising effect on the composition of bacteria. In most systems, the water exchange rates and organic loading applied for biological reasons allow for microbial regrowth in the rearing tanks. Hence, alternative approaches to reduce the chances of disease outbreaks are needed. This project pursues the concept of establishing and maintaining stable microbial systems. Water treatment technology for promoting K-selection, which is a selective pressure disfavouring the r-selected opportunists, has shown very promising results for several marine species in small scale experiments, but the up-scaling and optimization for flow through systems (FTS) and recirculating aquaculture systems (RAS) remains. The paradigm favouring a stable and elevated bacterial abundance is foreseen to reduce fish mortality and also reduce water treatment costs. This project will investigated fish health and microbial carrying capacity correlations as well as identifying treatment requirements to achieve a certain microbial stability.

Partners in the project is NTNU, Department of Biotechnology (coordinator), Hochschule für Technik und Wirtschaft, and Technical University of Denmark (DTU Aqua). The project runs for the period 2015-2018 and is financed by Research Council of Norway and is part of the EraNet COFASP.


MIRA – MIcrobially produced Raw materials for Aquafeed (2014-2018)

Marine microorganisms are a natural source of essential fatty acids, proteins, vitamins, minerals and other nutrients. Thus cultivated microorganisms are a sustainable resource for salmon feed ingredients on both short and long term.

The overall objective of this project is to establish new knowledge on the possibility of using biotechnological production systems for realization of bacteria and photosynthetic microalgae as sustainable resource for protein and EPA/DHA in salmon feed.

Secondary objectives:

1. Establish strains of R. opacus with the ability to synthesise DHA and incorporate it in storage lipids using a synthetic biology approach

2. Establish strains of microalgae with reduced antenna size and hence improved quantum yield and increased productivity by selection and gene editing

3. Evaluate microbial raw materials as feed ingredients in digestion and growth trials with salmon

4. Make an analysis of sustainability and social acceptance of GMO and non-GMO microbial biomass for fish feed

5. Disseminate the results to the scientific community, stakeholders and the general public

The project partners are a multidisciplinary team and include The Norwegian University of Science and Technology (NTNU) with Departments of Biotechnology, Biology, and Energy and Process Engineering-Industrial Ecology, SINTEF Fisheries and Aquaculture, SINTEF Materials and Chemistry, and international partners (IGV GmbH and Univ. Münster)

The project runs for the period 2014-2018 and is financed by Research Council of Norway.


Gnotobiotic cod larvae to unravel microbe-microbe and microbe-host interactions (2014-2016)

For most marine aquaculture species, and especially for reared cod, one of the main challenges is the stable production of high quality juveniles. The high and unpredictable mortality, which can amount to more than 80 % in the first weeks after hatching, is mainly due to unfavourable interactions with bacteria in the water.

In order to improve the survival and growth of cod larvae, we need a better understanding of the interactions that take place between the larvae and microbes, and between the microbes themselves. However, these host-microbe and microbe-microbe interactions are incredibly complex. This inherent complexity can be successfully reduced by applying gnotobiotic systems, which contain only known bacteria. By allowing cod larvae to develop under specific and known conditions, the effects of bacteria during a period of rapid growth and extensive gut development can be intensively studied.

This project is divided into three sub-projects:

  • Cod larvae reared under different microbial conditions will be analysed with regards to effects the microbiota have on growth, survival, gene expression and metabolomics.
  • Community structure of the microbiota associated with developing cod larvae, the function of r- and K-selected microbial communities, and also host responses to different microbial communities.
  • Determine complex microbe-host and microbe-microbe interactions in cod larvae by correlating different microscopic techniques at different resolutions.

This project is co-funded by NFR (HAVBRUK, 233865), NT-faculty NTNU and EU through FP7-PEOPLE-2013-IIF (project number 625655).


Lipid production and photosynthesis in the microalga Nannochloropsis oceanica (2013-2016)

The heterokont alga Nannochloropsis sp. has in the later years become a new model organism in algae research, mainly due to its ability to synthesize and store relatively large amounts of fatty acids. Nannochloropsis has also been studied from a photosynthetic perspective, but the link between fatty acid production and photosynthesis, which is the objective of this project, has so far not been studied in depth.

It is already known that environmental stress factors like changes in the nitrate and phosphate content of the cell medium, the salinity of the cell medium, temperature or changes in light intensity during cultivation of the algal cells have the ability of changing the lipid profile of the algae. In this project, the effect of oxygen deprivation, temperature, and light intensity will be investigated by analysing the lipid content and also the lipid composition on the algae. The gene expression under the different environmental influences will also be investigated, and so will the performance of the photosynthetic machinery. The ultimate goal of the project is to link the responses observed in the processes of lipid production, photosynthesis and gene expression to gain a better understanding of these important processes in Nannochloropsis.

One PhD candidate is currently working on this project, supported by the Faculty of Science and Technology and the Strategic Research Area at NTNU "Ocean Science and Technology".


Aerobic and anaerobic ammonium oxidation at high salinities (2012-2016)

Due to the environmental impact of aquaculture, it is essential to develop efficient treatment of potentially harmful effluents and byproducts. The recent development of water-recycling aquaculture farms has emphasized the need for water treatment in accordance with the quality demands of the fish, with tolerance limits as low as < 0,01 mg NH3-N/l. It is essential to obtain this quality even at oceanic salinities when producing marine species.

The objectives of the current project are: 1) To establish functional enrichment cultures capable of aerobic nitrification and of anaerobic ammonium oxidation with nitrite ("Anammox") at conditions up to marine oceanic salinities (34 ‰). 2) To study the phylogenetic composition and dynamics of the microbial communities involved in the adaptation to those high salt conditions. 3) To optimize full nitrification at those high salt concentrations and identify the bottlenecks in scaling up the processes for application in recycled marine aquaculture plants. 4) To evaluate the feasibility and start-up strategies for designing marine full scale biofilters for nitrification to protect fish in recycled plants.

One PhD candidate is currently working on this project, supported by a Faculty PhD scholarship.


Biological N removal from process waste water of a CO2 capture plant (2008-2010/-16)

Post-combustion CO2 capture by amine absorption (Photo design Sintef Process Technology)Post-combustion CO2 capture by amine absorption (Photo design Sintef Process Technology)

Combustion of fossil fuels constitutes a major man-made contribution to global warming of our planet due to the greenhouse effect of CO2. Post-combustion capture has been seen as the easy method to reduce emissions from large point sources such as power plants based on fossil fuels. Such capture may be achieved by absorption with amines. However, a significant operational problem at full scale will be gradual loss of amines due to irreversible side reactions. Recycled wash and process water must therefore be bled from the system to allow replenishment. This produced waste water may contain large amounts of ammonia as a major degradation product as well as contaminating levels of the actual amine applied. This is a special waste effluent that should be treated accordingly.


Biological N removal is a well established method in wastewater treatment, generally based on a two-step process: The first step denoted nitrification includes lithoautotrophic bacteria that will oxidise ammonium to nitrate. In the second step denoted denitrification, facultative heterotrophs reduce nitrate to nitrogen gas by anaerobic respiration.

Initial studies were focussed on developing suitable analytical procedures to avoid cross-interference between compounds in complex N-containing mixtures. Long-term model studies have been performed to establish efficient moving bed biofilm 1 L lab scale reactors, mainly using monoethanol amine (MEA) as a model compound, mixed with ammonia in our wastewater model mix. Acute toxicity of relevant amines has been tested separately for nitrifying and denitrifying biofilms. When interconnected in a so-called post-denitrification configuration, efficient N removal was obtained by adding ethanol as a carbon source for the dentrifying step. A pre-denitrification configuration with recycling from a second nitrifying reactor was then applied to utilize any carbon source available in the process water for the denitrification. In these model studies, successful N removal was established even with MEA as the only carbon source. Thus, this approach has been shown to be feasible. Other relevant amines are currently tested.

This project is run in close cooperaton with SINTEF Process Technology, financed as a part of SOLVit – an 8-year R&D program involving SINTEF, NTNU, Gasnova and Aker Clean Carbon, with the latter as coordinator. SOLVit's goal is to develop improved and cost-efficient methods for CO2 removal. Started 2008, its first phase will be summarised at the end of 2010.


BIONA - Biogas Reactor Technology for Norwegian Agriculture (2011-2014)

has the primary objective to make biogas reactor technology cost effective, robust and well adapted for use in Norwegian agriculture.

In order to reduce the greenhouse emissions in Norway, most of the manure should be treated in anaerobic digestion (AD) plants. The AD plant economy can be enhanced by increased biogas production obtained by co-digestion of energy rich substrates like fish ensilage, food waste or slaughter house waste. However, the AD process is sensitive to high concentrations of the ammonia produced by degradation of the protein rich substrates mentioned.

Microorganisms that tolerate high concentrations of ammonia are slow-growing and can easily be washed out of the biogas reactor. The development of ammonia tolerant microbes living in biofilms is proposed as a solutin to this problem. In the project the potential role of ammonia tolerante cultures will be analyzed and process design criteria for for ammonia tolerant systems suitable for Norwegian agriculture will be suggested.

It has been a general problem of bioprocess engineering that design criteria are rarely verified or validated by thorough analysis of the full scale plant during operation. Although plants may be functional at steady state, misconceptions of the actual microbial composition and distribution may lead to serious operational problems during instabilties and disturbances. Such a lack of essential microbial data reflects the classic lack of suitable methods when relevant microbes cannot be grown in pure culture. In the last decades, however, this problem has largely been overcome by new molecular genetic methods that may be applied even for nonculturable organisms in microbial communities.

The project is devided into three work packages:

WP1: Ammonia tolerant biogas processes
WP2: Sensor technology and process optimization
WP3: High rate biogas reactors of UASB type integrated with existing farm infrastructure.

The project is a cooperation between Bioforsk, Norwegian University of Life Sciences UMB, Telemark University College TUC and NTNU.

Wtihin this framework, it is our particular role at NTNU to contribute to the WP 3.1 Process analysis by performing microbial community analysis of relevant anaerobic ecosystems, primarily in cooperation with TUC (HiT) by analyzing their experimental anaerobic model digesters during operation. 


SOLBIOPTA - Biotechnological Production of Materials for Optimized Solar Cell Efficiency (2010-2013)



Solar energy is the most plentiful, least tapped energy reserve known and thus, improved terrestrial utilization of light and heat from the sun has the potential of supplying a significant proportion of mankind's future "clean" energy needs. As such, electricity generation through solar cells is an important part of this scenario. One of the most important scientific and technological challenges faced by the solar cell community ahead, regardless of solar cell concept chosen, is to make a breakthrough in terms of solar cell efficiency. One method to improve the performance of a solar cell, is to improve its light harvesting efficiency, i.e., to utilize larger portions of the spectrum, and to increase the absorption efficiency where absorption occurs


The project we will study the production and use of novel bio-nanomaterials from the microalgae diatoms in solar cell applications. The project describes highly multi-disciplinary research in a relatively new field, and will allow the participating partners to carry out potentially pioneering research. A joint scientific project aimed at producing materials for increased solar cell efficiencies using biotechnological methods, will bring together knowledge from both the traditional photovoltaic material science field and the bio-materials field. We aim to increase the fundamental understanding of key biological processes for production of novel bio-nanomaterial, and to evaluate how such materials may be used to improve solar cell efficiencies.

The project is organized in three sub-projects arranged chronologically, but with feedback serving as criteria for refinement of goals and for design of experiments. The three subprojects are:

SP 1: Biotechnological production of nanostructured oxides using diatoms

SP 2: Bio-nanooxide materials characterization and modification

SP3: Application of bio-nanooxides as light harvesting materials for solar cells

The project is a cooperation between the NTNU Departments Material Science and Engineering, Biotechnology, and Biology and SINTEF Materials and Chemistry. The project will have an interface towards the CEER Solar Cell Technology

Promicrobe - Microbes as positive actors for more sustainable aquaculture (2009-2013)


Larve of Atlantic cod and candidate probiotic bacteria (Photo montage:KJ Playfoot)Larve of Atlantic cod and candidate probiotic bacteria (Photo montage:KJ Playfoot)

Aquaculture is still facing a number of bottlenecks. To further develop aquaculture, the major bottlenecks need to be systematically removed. At the production level, unpredictable larval survival and larval/juvenile quality and robustness are major bottlenecks which have strong microbial components. With respect to microbial interference, we need to make use of the natural mutualistic symbiotic relationships that have evolved over million of years between the host and the microbial community. Hence, we need to understand the mutual and reciprocal interactions between them and use these interactions to the benefit of the viability and robustness of the fish under aquaculture conditions. This "join them" approach is contradictory to the traditional "beat them" strategy generally applied in microbial management used in human medicine, agriculture and aquaculture. This project suggests bringing together various European research groups that have contributed to some important methodological break-throughs that can be used in the study of host/microbe interactions and can help to disentangle the complex interplay between the different components of the aquaculture ecosystem. The work packages are directed towards the systematic gathering of novel information in relation to the axis host-host microbial community-system microbial community. It is anticipated that this novel information will allow developing new concepts that will be translated into new or adapted protocols to rear aquaculture organisms in a biological stable and economical efficient way.


The project is funded by the European Union, and has the following partners: Ghent University (coordinator), Belgium; Institut Français de Recherche pour l'Exploitation de la Mer, France; Wageningen University, Netherlands; Norwegian University for Science and Technology, Norway; SINTEF Materials and Chemistry, Norway; SINTEF Fisheries and Aquaculture, Norway; Flanders Institute for Biotechnology, Belgium. More information is found here.


NSTTT – Norwegian Seaweed Technology Center (2012 – 2012)

NSTTT has been established by SINTEF Aquaculture, with the Department of Biotechnology as one of the cooperating partners, in order to establish a platform of knowledge for sustainable, industrial seaweed cultivation and use in Norway. The main activity is development of large scale cultivation technology combined with complete utilization of the produced biomass, emphasizing energy, feed and food. It is the Center's opinion that cultivation and use of seaweeds should become a topic of high priority for the Trøndelag region.


Biorefinery Application (2011-2011)

As a part of our Seaweed Biorefinery Systems (SBS) strategy on seaweed utilization, agreement has been made with the company Seaweed Energy solutions for a pilot project on developing new ideas, concepts and proposals for future research foucussing on multiproduct biorefinery strategies such as combined production of ethanol as well as biogas.



Biogas production by cattle (Photo montage K. Østgaard)Biogas production by cattle (Photo montage K. Østgaard)

Biogas Trøndelag - Microbial methods for design and operation of local biogas facilities (2009-2010)


Biogas production by anaerobic fermentation may represent an efficient utilization of biodegradable wet organic waste. According to the Norwegian Ministry of Agriculture and Food (, our total energy potential of wet organic waste is about 6 TWh. Livestock manure constitutes 42 % of this, compared to 90 % for the EU region. We have previously studied biogas production from marine primary biomass consisting of brown seaweeds, while long-term cooperation with Bioskiva AS has handled a variety of aspects related to process optimization of anaerobic fermentation of cattle manure for total utilization.

From 2009 we participate in the Norwegian Research Council (NFR) "Brukerstyrt innovasjonsprosjekt" (BIP) project "Biogas Trøndelag" on biogas production from cow manure, coordinated by Fosen Næringshage AS and involving the newly formed company Biogass Fosen SA. By utilizing the pilot plant facilities at Bioskiva AS, long-term batch culture development of biogas producing microbial communities have been studied in particular at mesophilic conditions applying non-hygienized cow manure. In close cooperation with the project partner Sintef Biotechnology, chemical analysis of COD fractions as well as volatile fatty acids (VFA) by HPLC is applied to monitor the process. Denaturating Gradient Gel Electrophoresis (DGGE) as well as Fluorescent in situ hybridisation (FISH) is applied to analyse the microbial community, in particular how the methanogenic Archaea grow and develop over time. Preliminary results seem promising.

The project is supported as an integrated part of the ongoing NFR RENERGI programme innovation project: "Biogass Trøndelag: Helhetlig og lokalt tilpasset design av biogassanlegg" throughout 2009 and -10.


Cultures of different microalgae (Photo NTNU Info/Rune Petter Ness)Cultures of different microalgae (Photo NTNU Info/Rune Petter Ness)

Lipido - Optimizing Lipid Production by Planktonic Algae (2007-2011)

The Consortium will address a so far neglected biomass source for biofuel and energy production: cultivated planktonic algae. This novel, essentially carbon negative energy source holds a number of unrivalled possibilities in terms of yield of optimally utilizable biomass, flexibility in implementation of production units, and socio-economical benefits through genuinely synergic coupling to mitigation of carbon and nutrient emissions. Verification and realization of these potentials depends on providing necessary up-to-date knowledge through research on algal growth and lipid yield, culturing conditions, commercially interesting by-products, and economical and social feasibility analysis covering the whole production framework including downstream processes.


The main objective of the project will be to provide a proof-of-concept level evaluation of algae as a potential raw material for biodiesel. This will be done by:

1) Screening the most promising algal species for temperate environments

2) Optimizing their growth and lipid yield as functions of growth conditions

3) Testing the practical applicability of coupling algal culturing to CO2 emission mitigation

4) Screening commercially interesting by-products from biomass of selected species

Cultures of different microalgae (Photo NTNU Info/Rune Petter Ness)

As importantly, we aim at identifying the next steps of the verification of the concept at large scale, and will proceed in mapping industrial interest and related funding sources for this work.

The project is a cooperation between Finnish Environment Institute, Finland (coordinator); VTT Technical Research Centre of Finland, Finland; Norwegian University of Science and Technology, Norway; University of Oslo, Norway; Ludwig Maximilian University, Germany; Blue Lagoon, Iceland.

The project is funded by N-INNER , the Northern European Innovative Energy Research Programme, and more information on LIPIDO can be found here.


Ballast water – Evaluation of methods for treatment of microbes in ballast water (2005-2009)


The process of balast water loading and discharge.The process of balast water loading and discharge.

It is well documented that ballast water has served as an inoculum for introduced species world wide, and the consequences for release of alien species can be dramatic with complete disruption of ecosystem functions. All types of organisms can be transferred with ballast water, and include virus's, bacteria, and single celled and multicellular plants and animals. The International Martime Organisation has proposed rules for treatment of ballast water with limits for densities of released organisms. This treaty is under ratification. There are large uncertainties with today's technologies for treatment of ballast water, and the wide variety of type of organisms represents a special challenge. This goes particularly for single celled organisms (microbes), where the possibility for escaping the treatment is huge due to their high numbers and possibilities for "hiding" inside particles. Moreover, it is not only the disinfection methods, but the whole treatment regime which is decisive for the spread of alien species. Most technologies have focused on treatment during filling of ballast tanks, but because disinfection per definition is a dramatic decimation and not 100% mortality it will be possible for many types of organisms to recolonize the water before it is released. Knowledge on recolonization of ballast water during the time frame of transport is essential for treatment strategies.


The project will focus on some of the aspects mentioned above, and address both biological and technological aspects and with focus on microbes. The following topics are highlighted: 1) The significance of biotic and abiotic particles as refuges against disinfection agents. 2) The impact of disinfection for production of easily degradable substrate for heterotrophic bacteria. 3) Recolonization kinetics by heterotrophic bacteria after disinfection.

The project is funded by VISTA , which is StatoilHydro's basic research programme which is conducted in close collaboration with the Norwegian Academy of Science and Letters.

CODTECH - A process oriented approach to intensive production of marine juveniles with main emphasis on cod (2003-2008)


Close up of larvae of Atlantic cod (Photo: T. Bardal)Close up of larvae of Atlantic cod (Photo: T. Bardal)

The Atlantic cod (Gadus morhua) is an important candidate for marine aquaculture. FAO regards cod as one of the most promising new aquaculture species, and assume that the production could be at least 1-2 million tons per year by 2015. The present Strategic University Programme is a multidisciplinary biological-biotechnological-technological approach to some main challenges of intensive rearing of cod juveniles. Developments will be based on experience from seabass and seabream in Southern Europe and the current international status for cod.


The main objective of the programme is: To contribute to further technological improvement and education of highly competent dr. and master candidates in the field of intensive marine juvenile technology, with main emphasise on cod. Main tasks are: 1) Modelling, instrumentation, control and optimisation of hatchery processes; 2) Larval feed components; 3) Microbial interactions and control; 4) Controlled intensive first feeding and weaning of cod larvae.

Future aquaculture production should benefit from the same technological advancement within process control and automation as experienced in conventional process industry. Methods and principles of cybernetics will be used as a framework for developments of equipment, instrumentation and automation of the production process of cod juveniles. The experimental work is focused on feeding regime, the resulting microbial regime, their interactions, and their components. A main target will accordingly be to establish a feeding regime for cod larvae that is nutritionally and microbially acceptable and feasible for partial automation. For more information (in Norwegian).