RESEARCHERS INVOLVED IN ECODESIGN MBR
AALBORG UNIVERSITY

Nielsen, Per Halkjær, Professor
Section of Biotechnology
phn@bio.aau.dk 

Nielsen, Jeppe Lund, Associate Professor
Section of Biotechnology
jln@bio.aau.dk 

Nielsen, Kåre Lehmann, Associate Professor
Section of Biotechnology
kln@bio.aau.dk 

Nierychlo Marta, Laboratory Engineer
Section of Biotechnology
mni@bio.aau.dk 

Christensen, Morten Lykkegaard, Assistant Professor
Section of Chemistry
mlc@bio.aau.dk 

Vollertsen, Jes, Professor
Section of Environmental Engineering
jv@bio.aau.dk 

Rasmussen, Michael R. Associate Professor
Urban Water Research Group
mr@civil.aau.dk 

Wybrandt, Lisbeth, Laboratory Technician
Section of Chemistry
lw@bio.aau.dk 

Jørgensen, Mads Koustrup, Post doc
Section of Chemistry
mkj@bio.aau.dk 

Albertsen, Mads, Post doc
Section of Biotechnology
ma@bio.aau.dk 

Hansen, Susan Hove, PhD Fellow
Section of Biotechnology
shj@bio.aau.dk 

Ziegler, Anja Sloth, PhD Fellow
Section of Biotechnology
asn@bio.aau.dk 

Kjeldal, Henrik, Post doc
Section of Biotechnology
kjeldal@bio.aau.dk 

Karst, Søren Michael
Section of Biotechnology
smk@bio.aau.dk 

Hao, Liping
Section of Biotechnology
lh@bio.aau.dk  

Kamilla Agnethe Smith Hansen
Section of Biotechnology
​kas@bio.aau.dk        

RELATED PROJECTS

Nguyen, Hien, Post doc
Section of Biotechnology
hn@bio.aau.dk 

TECHNICAL UNIVERSITY OF DENMARK, DTU

Smets, Barth F., Professor
Dept. of Environmental Engineering
bfs@env.dtu.dk 

Sin, Gurkan, Associate Professor
DTU Chemical Engineering department
gsi@kt.dtu.dk

Iglesias, Miguel Mauricio, Post doc
DTU Chemical Engineering department
mmi@kt.dtu.dk 

Jensen, Marlene M, Post doc
Dept. of Environmental Engineering
mmaj@env.dtu.dk 

GTS (ADVANCED TECHNOLOGY GROUP)
DHI

Kristensen, Gert Holm, Head of innovation
www.dhigroup.com 
ghk@dhigroup.com 

DHI

Jørgensen, Per Elberg
Urban and Industry Department
www.dhigroup.com 
pjo@dhigroup.com 

Danish Technological Institute (DTI)
Rickers, Caroline Kragelund, Center for Chemistry and Water Technology
www.dti.dk 
cakr@teknologisk.dk 

COLLABORATION WITH FOREIGN UNIVERSITIES

Van Loosdrecht, Mark, Professor
Section of Environmental Biotechnology, Delft University of Technology, The Netherlands
www.bt.tudelft.nl 
M.C.M.vanLoosdrecht@tudelft.nl 

Wagner, Michael, Professor
Dept. of Microbial Ecology, University of Vienna, Austria
www.microbial-ecology.net 
wagner@microbial-ecology.net 

Leiknes, TorOve, Professor
Dep. Hydraulic and Environmental Engineering, Norwegian University of Science and Technology, Norway
www.ntnu.no 
torove@leiknes@ntnu.no 

In the below list you will find the members of the EcoDesign steering committee, who are responsible for coordinating the different work packages and partner contributions.

STEERING COMMITTE:

• Per Halkjær Nielsen (Centre director), Section for Biotechnology, AAU
• Jeppe Lund Nielsen, Section for Biotechnology, AAU
• Morten Lykkegaard Christensen (AAU), Section for Chemistry, AAU
• Marta Nierychlo (Scientific coordinator), Section for Biotechnology, AAU
• Barth Smets, Department of Environmental Engineering, DTU
• Per Elberg Jørgensen, Urban and Industry Department, DHI
• Caroline Kragelund Rickers, Center for Chemistry and Water Technology, DTI
• Nicolas Heinen, Alfa Laval A/S
• Erik Bundgaard, Krüger A/S
• Jan Riis Bovbjerg, Grundfos Biobooster A/S
• Dines Thornberg, BIOFOS A/S

The partners of the Ecodesign project will participate in the different research areas during the project period. Below you will find a list with the contact details of the partners involved in the Ecodesign project:

DANISH UNIVERSITIES AND GTS (ADVANCED TECHNOLOGY GROUP)

AALBORG UNIVERSITY

Per Halkjær Nielsen: phn@bio.aau.dk 
Jeppe Lund Nielsen: jln@bio.aau.dk 
Morten Lykkegaard Christensen: mlc@bio.aau.dk 

DANISH TECHNOLOGICAL INSTITUTE (DTI)

Caroline Kragelund Rickers: cakr@teknologisk.dk  

TECNICAL UNIVERSITY OF DENMARK, DTU

Barth F. Smets: bfs@env.dtu.dk 
Gürkan Sin: gsi@kt.dtu.dk 

DHI

Gert Holm Kristensen: ghk@dhigroup.com 
Per Elberg Jørgensen: pjo@dhigroup.com

COMPANIES

ALFA LAVAL A/S

Nicolas Heinen: nicolas.heinen@alfalaval.com

KRÜGER A/S

Erik Bundgaard: eb@kruger.dk 
Vibeke Borregaard: vrb@kruger.dk

GRUNDFOS BIOBOOSTER A/S

Jan Riis Bovbjerg: jriisbovbjerg@grundfos.com

VEOLIA ENVIRONNEMENT

Emmanuel Trouve: emmanuel.trouve@veolia.com

NOVOZYMES A/S

Svend Kaj Petersen: svep@novozymes.com

COLLABORATION WITH WASTEWATER TREATMENT PLANTS

AALBORG FORSYNING, KLOAK A/S

Jesper S. Pedersen: jp@aalborgforsyning.dk 
Helle Strandbæk: hes@aalborgforsyning.dk

BIOFOS

Dines Thornberg: dt@spvand.dk

COLLABORATION WITH FOREIGN UNIVERSITIES

DELFT UNIVERSITY OF TECHNOLOGY, TU-DELFT

Mark van Loosdrecht: M.C.M.vanLoosdrecht@tudelft.nl

NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY, NTNU

TorOve Leikner: torove.leiknes@ntnu.no

UNIVERSITY OF VIENNA

Michael Wagner: wagner@microbial-ecology.net 
 
EXTERNAL FINANCIAL FUNDING
 
THE DANISH COUNCIL FOR STRATEGIC RESEARCH

2017

Cokro, A.A., Y. Law, R.B.H. Williams, Y. Cao, P.H. Nielsen, and S. Wuertz (2017) Non-denitrifying polyphosphate accumulating organisms obviate requirement for anaerobic condition. Water Research (in press).

Neufeld, J., L. Sauder, M. Albertsen, K. Engel, J. Schwarz, P. Nielsen, and M. Wagner (2017): Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system. The ISME Journal (in press).

2016

Albertsen, M., S.J. McIlroy, M. Stokholm-Bjerregaard, S.M. Karst and P.H. Nielsen (2016): ‘Candidatus Propionivibrio aalborgensis’: a novel glycogen accumulating organism abundant in full-scale enhanced biological phosphorus removal plants. Frontiers in Microbiology 7: 1033. DOI: 10.3389/fmicb.2016.01033.

Arriaga, S., de Jonge, N., Nielsen, M.L., Andersen, H., Borregaard, V., Jewel, K., Ternes, T., Nielsen, J.L. (2016). Evaluation of a membrane bioreactor system as post-treatment waste water treatment for better removal of micropollutants. Water Research 107: 37-46.

Herbst, F-H., V. Lünsmann, H. Kjeldal, N. Jehmlich, A. Tholey, M. von Bergen, J.L. Nielsen, R.L. Hettich, J. Seifert, P.H. Nielsen (2016): Enhancing metaproteomics - The value of models and defined environmental microbial systems. Proteomics 16: 783-798.  DOI:10.1002/pmic.201500305.

Karst, S.M., M.S. Dueholm, S.J. McIlroy, R.H. Kirkegaard, P.H. Nielsen, M. Albertsen (2016) Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life. BioRxiv.doi: http://dx.doi.org/10.1101/070771.

Kindaichi, T., S. Yamaoka, R. Uehara, N. Ozaki, A. Ohashi, M. Albertsen, P.H. Nielsen, J.L. Nielsen. (2016): Phylogenetic diversity and ecophysiology of candidate phylum Saccharibacteria in activated sludge. FEMS Microbiology Ecology, 92, doi: 10.1093/femsec/fiw078.

Laureni, M., Falås, P., Robin, O., Wick, A., Weissbrodt, D.G., Nielsen, J.L., Ternes, T., Morgenroth, E., and Joss, A. (2016) Mainstream partial nitritation/anammox: long-term process stability and overall effluent quality at low temperatures. Water Research 101: 628-639.

Law, Y, RH Kirkegaard, AA Cokro, X Liu, K Arumugam, C Xie, M Stokholm-Bjerregaard, DI Drautz-Moses, PH Nielsen, S Wuertz, RBH Williams (2016): Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions. Scientific Rep. 6, 25719. doi:10.1038/srep25719.

McIlroy, S.J., Karst, S.M., Nierychlo, M., Dueholm, M.S., Albertsen, M., Kirkegaard, R.H., Seviour, R.J., and Nielsen, P.H. (2016): Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge. ISME J. doi:10.1038/ismej.2016.14.

Saunders AM, Albertsen M, Vollertsen J & Nielsen PH (2016): The activated sludge ecosystem contains a core community of abundant organisms. The ISME Journal 10, 11–20 doi:10.1038/ismej.2015.117.

Silva, A.F., S. Antunes, A. Saunders, F. Freitas, A. Vieira, P.H. Nielsen, M.T.B. Crespo, G. Carvalho (2016): Impact of sludge retention time on the fine composition of the microbial community and extracellular polymeric substances in a membrane bioreactor. Applied Microbiology and Biotechnology 100: 8507-8521. Doi 10.1007/s000253-016-7617-2.

Ziegler, AS, SJ McIlroy, P Larsen, M Albertsen, AA Hansen, N Heinen, and PH Nielsen (2016): Dynamics of the fouling layer microbial community in a membrane bioreactor. PloSONE. DOI: 10.1371/journal.pone.0158811.

Zielińska, M., Rusanowska, P., Jarząbek, J., and Nielsen, J.L. (2016). Community dynamics of denitrifying bacteria in full-scale wastewater treatment plants. Environmental Technology, 18: 2358-2367.

Herbst, F., Lünsmann, V., Kjeldal, H., Jehmlich, N., Tholey, A., von Bergen, M., Nielsen, J.L., Hettich, R.L., Seifert, J., and Nielsen, P.H. Enhancing Metaproteomics - The value of models and defined environmental microbial systems. Proteomics, 16(5):783-98.

Kjeldal, H., Zhou, N., Wissenbach, D.K., von Bergen, M., Gough, H., and Nielsen, J.L. Genomic, proteomic and metabolite characterization of gemfibrozil-degrading organism Bacillus sp. GeD10. Environmental Science and Technology, 50(2): 744-755.

McIlroy, S.J., Karst, S.M., Nierychlo, M., Dueholm, M.S., Albertsen, M., Kirkegaard, R.H., Seviour, R.J., and Nielsen, P.H. (2016) Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge. ISME J., in press.

McIlroy, S.J., Szyszka, A., Starnawski, P., Saunders, A.M., Nierychlo, M., Nielsen, P.H., and Nielsen, J.L. (2016): Identification of active denitrifiers in full-scale nutrient removal wastewater treatment systems. Environmental Microbiology 18(1): 50-64.

2015

Albertsen M, Karst SM, Ziegler AS, Kirkegaard RH and Nielsen PH (2015): Back to basics – the influence of DNA extraction and primer choice on phylogenetic analysis in activated sludge communities. PLoSONE 10(7): e0132783.

Chen, X., Casas, M.E., Nielsen, J.L., Wimmer, R., and Bester, K. (2015): Identification of Triclosan-O-Sulfate and other transformation products of Triclosan formed by activated sludge. Science of the Total Environment 505: 39-46.

Chen, X., Vollertsen, J., Nielsen, J.L., Gieraltowska, A., and Bester, K. (2015): Degradation of PPCPs in activated sludge from different WWTPs in Denmark. Ecotoxicology 24(19): 2073-2080.

Christensen M. L. Filtration and Dewatering in Wastewater Treatment (2015): Filtration 15(3): 162-165.

Christensen M. L. Keiding, K. Nielsen P.H. Jørgensen, M. K. (2015): Dewatering in biological wastewater treatment: a review. Water research 82: 14-24.

Daims, H., E.V. Lebedeva, P. Pjevac, P. Han, C. Herbold, M. Albertsen, N. Jehmlich, M. Palatinszky, J. Vierheilig, A. Bulaev, R.H. Kirkegaard, M. von Bergen, T. Rattei, B. Bendinger, P.H. Nielsen, and M. Wagner. (2015): Complete nitrification by Nitrospira bacteria. Nature DOI: 10.1038/nature16461.

Dueholm, MS, M. Albertsen, M. Stokholm-Bjerregaard, S.J. McIlroy, S.M. Karst and P.H. Nielsen (2015): Complete genome sequence of the bacterium Aalborg_AAW-1 Representing a novel family within the candidate phylum SR1. Genome Announcements 3(3):e00624-15. DOI: 10.1128/genomeA.00624-15.

Dueholm, M.S., Marques, I.G., Karst, S.M., D'Imperio, S., Tale, V.P., Lewis, D., Nielsen, P.H., and Nielsen, J.L. (2015): Molecular Techniques Provide Intelligence on the Bioaugmentation Strains in Activated Sludge Augmented with Pseudomonas monteilii SB3078 and SB3101 for Enhanced BTEX Degradation. Bioresource Technology 186: 192-199.

El-Hamid, A. Elawady, M., El-Ghaffar M., Rabie, A, Larsen P. Christensen M.L. (2015): Surface Modification of Reverse Osmosis Membranes By Zwitterionic polymer for Reducing Biofouling. Water Science and Technology: Water Supply DOI: 10.2166/ws.2015.055.

Herbst, F-H., V. Lünsmann, H. Kjeldal, N. Jehmlich, A. Tholey, M. von Bergen, J.L. Nielsen, R.L. Hettich, J. Seifert, P.H. Nielsen (2015): Enhancing metaproteomics - The value of models and defined environmental microbial systems. Proteomics DOI: 10.1002/pmic.201500305.

Jørgensen M.K. Kujundzic E, Greenberg A. R. (2015): Effect of pressure on fouling of microfiltration membranes by activated sludge, Desalination and Water Treatment DOI: 10.1080/19443994.2015.1005695.

van Kessel, M.A.H.J, D.R. Speth, M.Albertsen, P.H. Nielsen, H.J.M. O. den Camp, B. Kartal, M.S.M. Jetten, S. Lücker. (2015): Complete nitrification by a single microorganism. Nature DOI: 10.1038/nature16459.

Koch, H, S Lücker, M Albertsen, K Kitzinger, C Herbold, E Spieck, PH. Nielsen, M Wagner, and H Daims (2015): Unexpected functional versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. PNAS DOI/10.1073/pnas.1506533112.

Laureni, M., Weissbrodt, D.G., Szivák, I., Robin, O., Nielsen, J.L., Morgenroth, E., and Joss, A. (2015): Activity and growth of anammox sludge on aerobically pre-treated municipal wastewater. Water Research 80: 325-336.

Madsen, A.M., Zervas, A., Tendal, K., and Nielsen, J.L. (2015): Microbial diversity in bioaerosol samples causing ODTS compared to reference bioaerosol samples as measured using Illumina sequencing and MALDI-TOF. Environmental Research 140: 255-267.

Mauricio-Iglesias, M., Vangsgaard, A. K., Gernaey, K. V., Smets BF & Sin, G. (2015): A novel control strategy for single-stage autotrophic nitrogen removal in SBR. Chemical Engineering Journal 260: 64–73.

McIlroy, SJ, T. Awata, M. Nierychlo, M. Albertsen, T. Kindaichi and PH Nielsen (2015): Characterisation of the in situ ecophysiology of novel phylotypes in nutrient removal activated sludge treatment plants. PLoSONE 10(9): e0136424. DOI: 10.1371/journal.pone.0136424.

McIlroy, SJ, A Lapidus, TR Thomsen, J Han, M Haynes, E Lobos, M Huntemann, A Pati, NN Ivanova, V Markowitz, S Verbarg, T Woyke, H-P Klenk, N Kyrpides and PH Nielsen (2015): High quality draft genome sequence of Meganema perideroedes str. Gr1T and a proposal for its reclassification to the family Meganemaceae fam. nov. Standard in Genomic Science (SIGS), DOI: 10.1186/s40793-015-0013-1.

McIlroy, S.J., T. Nittami, E. Kanai, J. Fukuda, A.M. Saunders and P.H. Nielsen (2015): Reappraisal of the phylogeny and FISH probes for the analysis of the Competibacteraceae in wastewater treatment systems. Environ. Microbiol. Reports 7: 166-74.

McIlroy SJ, Saunders AM, Albertsen M, Nierychlo M, McIlroy B, Hansen AA, Karst SM, Nielsen JL, Nielsen PH (2015): MiDAS: the field guide to the microbes of activated sludge. Database bav062. DOI: 10.1093/database/bav062.

Munck, C., M. Albertsen, A. Telke, M. Ellabaan, P.H. Nielsen, M.O.A. Sommer (2015): Limited dissemination of the wastewater treatment plant core resistome. Nature Communication, DOI: 10.1038/ncomms9452.

Nguyen, HTT, R Kristiansen, M Vestergaard, R Wimmer, and PH Nielsen (2015): Intracellular accumulation of glycine in polyphosphate-accumulating organisms in activated sludge – a novel storage mechanism under dynamic anaerobic-aerobic conditions. Appl. Environ. Microbiol. 81: 4809-4818. DOI: 10.1128/AEM.01012-15.

Nousiainen, A.O., Björklöf, K., Sagarkar, S., Nielsen, J.L., Kapley, A., and Jørgensen, K.S. (2015): Bioremediation strategies for atrazine removal in the boreal groundwater zone. Applied Microbiology and Biotechnology 99:10249-10259.

Poorasgari E., Bugge T.V. Christensen M.L., Jørgensen M.K. (2015): Compressibility of fouling layers in membrane bioreactors. Journal of Membrane Science. 475, 65-70.

Saunders AM, Albertsen M, Vollertsen J & Nielsen PH (2015): The activated sludge ecosystem contains a core community of abundant organisms. The ISME Journal DOI: 10.1038/ismej.2015.117.

Urakawa, H., Garcia, J.C., Nielsen, J.L., Le, V.Q., Kozlowski, J.A., Stein, L.Y.,  Lim, C.K., Pommerening-Röser, A., Martens-Habbena, W., Stahl, D.A., Klotz, M.G. (2015): Nitrosospira lacus sp. nov., a psychrotolerant ammonia-oxidizing bacterium from sandy lake sediment. International Journal of Systematic and Evolutionary Microbiology 65:242-250.

Zhou, N., Kjeldal, H., Gough, H.L., and Nielsen, J.L. (2015): Identification of putative genes involved in bisphenol A degradation using differential protein abundance analysis of Sphingobium sp. BiD32. Environmental Science & Technology 49(20):12232-41.

2014

Amiri, S., Duroux, L., Nielsen, J.L., Nielsen, A.H., Yu, D., and Larsen, K.L. (2014): Preparation and Characterization of a Temperature-Sensitive Nonwoven Poly (propylene) with Antibacterial Properties. Journal of the Textile Institute 105(3):327-336 DOI:10.1080/00405000.2013.839355.

Behrendt, L., Nielsen, J.L., Sørensen, S.J., Larkum, A.W.D., Winther, J.R., and Kühl, M. (2014): Rapid TaqMan-based Quantification of Chlorophyll d-containing Cyanobacteria in the Genus Acaryochloris. Applied and Environmental Microbiology 80(10):3244-3249 DOI: 10.1128/AEM.00334-14.

Domingo-Félez C., A. G. Mutlu, M.M. Jensen, B. F. Smets. (2014): Aeration strategies to mitigate nitrous oxide emissions from single-stage nitritation/anammox reactors. Environ. Scie. Technol. 48: 920–929 DOI: 10.1021/es501819n.

Dueholm, M.S., Albertsen, M., D'Imperio, S., Tale, V.P., Lewis, D., Nielsen, P.H., and Nielsen, J.L. (2014): Complete Genome Sequences of Pseudomonas monteilii SB3078 and SB3101, Two Benzene-, Toluene-, and Ethylbenzene-Degrading Bacteria Used for Bioaugmentation. GenomeA 2(3): e00524-14.

Dueholm, M.S., Albertsen, M., D'Imperio, S., Tale, V.P., Lewis, D., Nielsen, P.H., and Nielsen, J.L. (2014): Complete Genome of Rhodococcus pyridinivorans SB3094, a Methyl-Ethyl-Ketone-Degrading Bacterium Used for Bioaugmentation. GenomeA 2(3): e00525-14.

Gilbert, E.M., S. Agrawal, S.M. Karst, H. Horn, P.H. Nielsen, S. Lackner (2014): Low temperature partial nitritation/anammox in a moving bed biofilm reactor treating low strength waste water. Environmental Science & Technology 48: 8784-8792.

Jensen S.H., A. Stensballe, P.H. Nielsen, F.-A. Herbst (2014): Metaproteomics: Evaluation of protein extraction from activated sludge. Proteomics 14(21-22): 2535-2539.

Jørgensen M. K., Keiding, K., Christensen M.L., (2014): On the reversibility of cake buildup and compression in a membrane bioreactor. Journal of Membrane Science 455: 152-161.

Jørgensen M. K., Pedersen M. T., Christensen M.L., Ruby T. (2014): Dependence of Shear and Concentration on Fouling in a Membrane Bioreactor with Rotating Membrane Discs. AIChE J 60: 706-715.

Kjeldal, H., Pell, L., Pommerening-Röser, A., and Nielsen, J.L. (2014): Influence of p-cresol on the proteome of the autotrophic nitrifying bacterium Nitrosomonas eutropha C91 Archives of Microbiology 196 (7): 497-511.

Koch, H., A. Galushko, M. Albertsen, A. Schintlmeister, C. Dorninger, S. Lücker, E. Pelletier, D. LePaslier, E. Spieck, A. Richter, P.H. Nielsen, M. Wagner, H. Daims (2014): Growth of nitrite-oxidizing bacteria by the knallgas metabolism. Science 345: 1052. DOI: 10.1126/science. 1256985.

Lanham, A.B., A. Oehmen, A.M. Saunders, G. Carvalho, P.H. Nielsen, M.A. M. Reis (2014): Metabolic modelling of full-scale enhanced biological phosphorus removal sludge. Water Research 66: 283-295.

Lorenzen S. Hinge M. Christensen M. L. Keiding K (2014): Filtration of core-shell colloids in studying the dewatering properties of water-swollen materials. Chemical Engineering Science, 116: 558-566.

Lou, M.A., P. Larsen, P.H. Nielsen and S.N. Bak (2014): Influence of shear on nitrification rates in a membrane bioreactor. Wat. Sci. Tech. 69(8): 1705-1711.

McIlroy, S.J., Albertsen, M., Andresen, E.K., Saunders, A.M., Kristiansen, R., Stokholm-Bjerregaard, M., Nielsen, K.L. and P.H. Nielsen (2014): “Candidatus Competibacter”-lineage genomes retrieved from metagenomes reveal functional metabolic diversity. ISME J. 8: 613-624.

Nilsson, F., M. Hagman, A.T. Mielczarek, P.H. Nielsen, K. Jönsson (2014): Application of ozone in full-scale to reduce filamentous bulking sludge at Öresundsverket WWTP. Ozone: Science & Engineering 36: 238–243.

Poorasgari E. König K, Fojan P. Keiding K. Christensen M. L. (2014): Fouling of enhanced biological phosphorus removal-membrane bioreactors by humic-like substances. Chemosphere. 117: 144-150.

Poorasgari E., Larsen P., Zheng X., Nielsen P.H., Keiding K., Christensen M. L. (2014): Irreversible fouling of membrane bioreactors due to formation of a non-biofilm gel layer. Water Science and Technology, 69: 1641-1647.

Suhr, K.I., Pedersen, L.F., and Nielsen, J.L. (2014): End-of-pipe single-sludge denitrification in pilot-scale recirculating aquaculture systems. Aquacultural Engineering 62: 28-35. DOI: 10.1016/j.aquaeng.2014.06.002.

Vangsgaard, A. K., Mauricio-Iglesias, M., Gernaey, K. V., & Sin, G. (2014): Development of novel control strategies for single-stage autotrophic nitrogen removal: A process oriented approach. Computers and Chemical Engineering, 66: 71-81. 

2013

Garcia, J.C., Urakawa, H., Le, V.Q., Stein, L.Y., Klotz, M.G., and Nielsen, J.L. (2013). Draft Genome of Nitrosospira sp. Strain APG3, a Psychrotolerant Ammonia-Oxidizing Bacterium Isolated from Sandy Lake Sediment. 

Albertsen M., Stensballe A., Nielsen K.L. and Nielsen P.H. (2013): Digging into the extracellular matrix of a complex microbial community using a combined metagenomic and metaproteomic approach. Wat. Sci. Tech. 67(7): 1650-1656.

Albertsen, M., Hugenholtz, P., Skarshewski, A., Nielsen, K.L., Tyson, G.W., Nielsen, P.H. (2013): Recovery of genomes from rare uncultured bacteria by differential coverage binning of multiple deep metagenomes. Nat. Biotech. 31(6): 533-8.

Almeida, B., Kjeldal, H., Lolas, I.B.Y., Knudsen, A., Carvalho, G., Nielsen, K.L., Crespo, T.B., Stensballe, A., and Nielsen, J.L. (2013): Quantitative proteomic analysis of ibuprofen-degrading Patulibacter sp. strain I11. Biodegradation 24(5): 615-630.

Kindaichi, T., Nierychlo, M., Kragelund, C., Nielsen, J.L., and Nielsen, P.H. (2013): High and stable substrate specificities of microorganisms in enhanced biological phosphorous removal plants. Environmental Microbiology 15(6): 1821-1831.

Kristiansen R., H.T.T. Nguyen, A.M. Saunders, J.L. Nielsen, R.Wimmer, V.Q. Le, S.J. McIlroy, S. Petrovski, R.J. Seviour, A. Calteau, K.L. Nielsen, P.H. Nielsen (2013): A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal. ISME Journal. 7(3): 543-54 DOI: 10.1038/ismej.2012.136.

McIlroy, S.J., Kristiansen, R., Albertsen, M., Karst, S.M., Rossetti, S., Nielsen, J.L., Tandoi, V., Seviour, R.J., and Nielsen, P.H. (2013): Metabolic models based on genomic sequence data from metagenomic libraries and axenic strains of the lipid accumulating filamentous bacterium Candidatus ‘Microthrix parvicella’. ISME Journal 7(6): 1161-1172.

McIlroy S.J., Kristiansen R., M. Albertsen, S.M. Karst, S. Rossetti, J.L. Nielsen, V. Tandoi, R.J. Seviour and P.H. Nielsen (2013): Metabolic model for filamentous “Candidatus Microthrix parvicella” based on genomic and metagenomic analyses. ISME Journal. DOI:10.1038/ismej.2013.6.

Mielczarek, A.T., Nguyen H.T.T., Nielsen, J.L., and Nielsen, P.H. (2013): Population dynamics of bacteria involved in enhanced biological phosphorus removal in Danish wastewater treatment plants.Water Research 47(4): 1529-1544.

Mielczarek, A.T., Saunders, A.M., Larsen, P., Albertsen, A., Stevenson, M., Nielsen, J.L. and Nielsen, P.H. (2013): The Microbial Database for Danish wastewater treatment plants with nutrient removal (MiDas-DK) – a tool for understanding activated sludge population dynamics and community stability. Wat. Sci. Tech. 67(11): 2519-2526.

Mutlu, A.G., Vangsgaard, A.K., Sin, G. & Smets, B.F. (2013): An operational protocol for facilitating start-up of single-stage autotrophic nitrogen removing reactors based on process stoichiometry. Water Sci. Technol. 68(3): 514-21.

Pellicer-Nàcher, C. , Domingo-Félez, A. G. Mutlu, and B. F. Smets. (2013): Critical assessment of methods for the extraction of extracellular polymeric substances from mixed culture biomass. Wat. Res. DOI: 10.1016/j.watres.2013.06.026.

Saunders, A.M., P. Larsen and P.H. Nielsen (2013) Comparison of nutrient-removing microbial communities in activated sludge from full-scale MBRs and conventional plants. Wat. Sci. Tech. 68(2): 366-371.

Seifert, J.F.-A. Herbst, P.H. Nielsen, F.J. Planes, M. Ferrer, M. von Bergen (2013): Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities. Proteomics 13(18-19): 2786-804.

Smets, B.F. (2013): Spatial structuring of microbial communities – at the micro- to millimetre scale. Microb. Biotechnol. 6: 10-11. DOI:10.1111/1751-7915.12014.

Vangsgaard, A.K., Mauricio-Iglesias, M., Gernaey, K.V., Smets, B.F. & Sin, G. (2013): Control of a Biological Nitrogen Removal Process in an Intensified Single Reactor Configuration. Computer Aided Chemical Engineering. 32: 769-774.

Vangsgaard, A.K., Mauricio-Iglesias, M., Valverde-Perez, B., Gernaey, K.V. & Sin, G. (2013): pH variation and influence in an autotrophic nitrogen removing biofilm system using an efficient numerical solution strategy. Water Sci. Technol. 67(11): 2608-15.

Vangsgaard, A.K., Mutlu, A.G., Gernaey, K.V., Smets, B.F. & Sin, G. (2013): Calibration and validation of a model describing complete autotrophic nitrogen removal in a granular SBR system. J. Chem. Technol. Biotechnol. 88(11): 2007-2015.

2012

Albertsen M., Hansen L.B.S., Saunders A.M., Nielsen P.H., Nielsen K.L. (2012): A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal. ISME Journal 6: 1094-1106.

Bugge, T.W., M. K. Jørgensen, M. L. Christensen, K. Keiding, (2012): Modeling cake build-up under TMP step filtration in a membrane bioreactor: Cake compressibility is significant. Water Research, 46: 4330-4338.

Jacobsen, P.A.L., Nielsen, J.L., Juhl, M.V., Theilgaard, N., Larsen, K.L. (2012): Grafting cyclodextrins to calcium phosphate ceramics for biomedical applications J Incl Phenom Macrocycl Chemistry 72: 173-181.

Jørgensen, M. K, Bugge, T. V, Keiding K. (2012): Modeling approach to determine cake buildup and compression in a high-shear membrane bioreactor. Journal of Membrane Science, 409-410: 335-345.

Kristiansen, R., Nguyen H.T.T., Saunders, A.M., Nielsen, J.L., Wimmer, R., Le Quy, V., McIlroy, S.J., Petrovski, S., Seviour, R.J., Calteau, A., Nielsen, K.L., and Nielsen, P.H. (2012): A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal. ISME Journal 7(3): 543-554.

Kristiansen, A., Saunders, A.M., Hansen, A.A., Nielsen, P.H., and Nielsen, J.L. (2012): Community structure of bacteria and fungi in pig confinement building bioaerosols.  FEMS Microbiological Ecology 80: 390-401.

Lolas, I.B., Chen, X., Bester, K., and Nielsen, J.L. (2012): Identification of triclosan- degrading bacteria using stable isotope probing, fluorescence in situ hybridization and microautoradiography.Microbiology 158: 2796-2804.

Mielczarek, A.T., C. Kragelund, P.S. Eriksen and P.H. Nielsen (2012): Population dynamics of filamentous bacteria in Danish wastewater treatment plants with nutrient removal. Water Research 46 (12): 3781-3795.

Nguyen, H.T.T., J.L. Nielsen and P.H. Nielsen (2012): ‘Candidatus Halomonas phosphatis’, a novel polyphosphate-accumulating organism in full-scale enhanced biological phosphorus removal plants. Environ. Microbiol. 14(10): 2826-2837.

Nielsen, J.L., Nguyen, H.T.T., Meyer, R.L., P.H. Nielsen (2012): Identification of glucose-fermenting bacteria in a full-scale enhanced biological phosphorus removal plant by stable isotope probing. Microbiology 158: 1818-1825.

Nielsen, PH AM Saunders, AA Hansen, P Larsen, JL Nielsen (2012): Microbial communities involved in enhanced biological phosphorus removal from wastewater - a model system in environmental biotechnology. Current Opinion in Biotechnology 23: 452-459.

Sveegaard, S.G., K. Keiding, M. L. Christensen, (2012): Compression and swelling of activated sludge cakes during dewatering. Water Research 46: 4999-5008.

Vangsgaard, A.K., Mauricio-Iglesias, M., Gernaey, K.V., Smets, B.F. & Sin, G. (2012): Sensitivity analysis of autotrophic N removal by a granule based bioreactor: Influence of mass transfer versus microbial kinetics. Bioresource Technol. 123: 230-241.

2011

Chen, X., Nielsen, J.L., Furgal, K., Liu, Y., Lolas, I.B.Y., and Bester, K. (2011): Biodegradation of triclosan and formation of methyl-triclosan in activated sludge under aerobic conditions. Chemosphere 84: 452-456.

Dominiak, D.M., Nielsen, J.L., and Nielsen, P.H. (2011): Extracellular DNA is abundant and important for microcolony strength in mixed mirobial biofilms. Environmental Microbiology 13: 710-721.

Jensen, H.S, Lens, P.N.L., Nielsen, J.L., Bester, K., Nielsen, A.H., Hvitved-Jacobsen, T., and Vollertsen, J. (2011): Growth kinetics of hydrogen sulfide oxidizing bacteria in corroded concrete from sewers. Journal of Hazardous Materials 189: 685-691.

Kragelund, C, T.R. Thomsen, A.T. Mielczarek, and P.H. Nielsen (2011): Eikelboom’s morphotype 0803 in activated sludge belongs to genus Caldilinea in the phylum Chloroflexi. FEMS Microbiol. Ecology 76(3): 451-462.

Kristiansen, A., Lindholst, S., Feilberg, A., Nielsen, P.H., Neufeld, J.D., and Nielsen, J.L. (2011): Butyric acid and dimethyl disulfide assimilating microorganisms in a biofilter treating air emissions from a livestock facility.  Applied and Environmental Microbiology 77: 8595-8604.

Kristiansen, A., Pedersen, K.H., Nielsen, P.H., Nielsen, L-P., Nielsen, J.L., and Schramm, A. (2011): Bacterial community structure of a full-scale biofilter treating pighouse exhaust air.  Systematic and Applied Microbiology 34: 344-352.

Mußmann, M., Brito, I., Pitcher, A., Damsté, J.S.S., Hatzenpichler, R., Richter, A., Nielsen, J.L., Nielsen, P.H., Müller, A., Daims, H., Wagner, M., and Head, I.M. (2011): Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but do not live primarily from autotrophic ammonia oxidation. PNAS 108(40): 16771-16776.

Nguyen, H., V. Le, A.A. Hansen, J.L. Nielsen, P.H. Nielsen (2011): High diversity and abundance of putative polyphosphate-accumulating Tetrasphaera-related bacteria in activated sludge systems. FEMS Microbiology Ecology 76(2): 256-267.

2010
 
Christensen, M.L., Dominiak, D.M., Nielsen, P.H., Sedin M., Keiding, K. (2010): Gravitational drainage of compressible organic materials. AIChE Journal 56(12): 3099-3108.

Christensen, M.L., Petersen, R.R. and Jørgensen, L.B. (2010): Simulation of sludge dewatering on belt filters. Water Science and Technology 61(12): 3162-3168.

Kragelund, C., Nilsson, B., Eskilsson, K., Bøgh, A.M. and Nielsen, P.H. (2010): Full-scale control of Mycolata foam by FEX-120 addition. Wat. Sci. Tech. 61: 2443-2450.

Nielsen, P.H., Mielczarek, A.T., Kragelund, C., Nielsen, J.L., Saunders, A.M., Kong, Y., Hansen, A.A. and Vollertsen, J. (2010): A conceptual ecosystem model of microbial communities in enhanced biological phosphorus removal plants. Wat. Res. 44(17): 5070-5088.

Pedersen, L.-F., Pedersen, P.B., Nielsen, J.L. and Nielsen, P.H. (2010): Long term/low dose formalin exposure to small-scale recirculation aquaculture systems. Aquacultural Engineering 4: 1-7.

Sun, S.P., Pellicer i Nàcher, C., Merkey, B., Zhou, Q., Xia, S.-Q., Yang, D.-H., Sun, J.-H. and Smets, BF. (2010): Effective Biological Nitrogen Removal Treatment Processes for Domestic Wastewaters with Low C/N Ratios: A Review. Environmental Engineering Science 27(2): 111-126.

Vlaeminck, S.E., Terada, A., Smets, BF., De Clippeleir, H., Schaubroeck, T., Bolca, S., Demeestere, L., Mast, J., Boon, N., Carballa, M. and Verstraete, W. (2010): Aggregate Size and Architecture Determine Microbial Activity Balance for One-Stage Partial Nitritation and Anammox. Applied and Environmental Microbiology 76(3): 900-909.

2009

Hesselsoe, M., Füreder, S., Schloter, M., Bodrossy, L., Iversen, N., Roslev, P., Nielsen, P.H., Wagner, M. and Loy, A. (2009): Isotope array analysis of Rhodocyclales uncovers functional redundancy and versatility in an activated sludge. ISME J. 3: 1349-1364.

Nielsen, P.H., Kragelund, C., Seviour, R.J. and Nielsen, J.L (2009): Identity and ecophysiology of filamentous bacteria in activated sludge. FEMS Microbiology Reviews 33: 969-998.

BOOKS:

2017

Gough, H.L., and Nielsen, J.L. Bioaugmentation, In Hydrocarbon and Lipid Microbiology Protocols, McGenity, Timmis, Nogales Fernández (Eds.) Springer Journals. In press.

2016

Dueholm M.S. and P.H. Nielsen (2016): Amyloids - A neglected child of the slime. Chapter in “The Perfect Slime: Microbial Extracellular Polymeric Substances (EPS)”, Eds: H.-C. Flemming, T.R. Neu and J. Wingender. ISBN: 9781780407418, IWA Publishing, London, UK.

van Loosdrecht, M.C.M., P.H. Nielsen, C.M. Lopez-Vazquez and D. Brdjanovic. (2016): “Experimental Methods in Wastewater Treatment”. Editors. ISBN: 9781780404745 (Hardback), ISBN: 9781780404752 (eBook). Published by IWA Publishing, London, UK. 2016.

Nielsen, J.L., Seviour, R., and Nielsen, P.H. (2016): Microscopy, In Experimental Methods in Wastewater Treatment (2016), van Loosdrecht, M.C.M., Nielsen, P.H., Lopez Vazquez, C.M., and Brdjanovic, D. (Eds). IWA publishing, London. UK. ISBN: 9781780404745 (Hardback), ISBN: 9781780404752 (eBook).

Karst S.M., Albertsen M., Kirkegaards R.H., Dueholm M.S., Nielsen P.H. (2016): Molecular Methods, In Experimental Methods in Wastewater Treatment (2016), van Loosdrecht, M.C.M., Nielsen, P.H., Lopez Vazquez, C.M., and Brdjanovic, D. (Eds). IWA publishing, London. UK. ISBN: 9781780404745 (Hardback), ISBN: 9781780404752 (eBook).

Gough, H.L., and Nielsen, J.L. Bioaugmentation, In Hydrocarbon and Lipid Microbiology Protocols, McGenity, Timmis, Nogales Fernández (Eds.) Springer Journals. In press.

2015

Nierychlo, M., Nielsen, J.L., and Nielsen, P.H. (2015): Studies of the Ecophysiology of Single Cells in Microbial Communities by (quantitative) Microautoradiography and Fluorescence in situ Hybridization (MAR-FISH). In Hydrocarbon and Lipid Microbiology Protocols, McGenity et al. (eds.), Springer Protocols Handbooks, DOI 10.1007/8623_2015_66, Springer-Verlag Berlin Heidelberg, 2015.

2014

Nielsen, P.H. and C. McMahon (2014): Microbiology and microbial ecology of the activated sludge process. Chapter 4 (p. 53-75) in D. Jenkins and J. Wanner (eds): Activated sludge - 100 years and counting. IWA Publishing. ISBN: 9781780404936.

2010

Wanner, J., Kragelund, C. and Nielsen P.H. (2010): Microbiology of bulking. In: Microbial Ecology of Activated Sludge. Seviour, R. and Nielsen, P.H. (eds.) IWA Publishing Company, London, UK p. 191-214.

Seviour, R. and Nielsen, P.H. (2010): Microbial Ecology of Activated Sludge. IWA Publishing Company, London, UK. Editors. ISBN: 9781843390329.

Seviour, R.J. and Nielsen, P.H. (2010): Microbial Communities in activated sludge plants. In: Microbial Ecology of Activated Sludge. Seviour, R. and Nielsen, P.H. (eds.) IWA Publishing Company, London, UK p. 95-126.

Nielsen, J.L. and Nielsen, P.H. (2010): Combined microautoradiography and fluorescence in situHybridization (MAR-FISH) for the identification of metabolically active microorganisms. In: Microbiology of Hydrocarbons, Oils, Lipids (Ed. K.N. Timmis), Springer-Verlag GmbH Berlin Heidelberg p. 4093-4102.

2009

Nielsen, J.L. and Hansen, A.A. (2009): Identification of denitrifying microorganisms in activated sludge by FISH. In: FISH Handbook for Biological Wastewater Treatment: Identification and quantification of microorganisms in activated sludge and biofilms by FISH. P.H. Nielsen; H. Daims; H. Lemmer (eds.) 1. ed. IWA Publishing Company, London, UK p. 19-24.

Nielsen, J.L. (2009): Protocol for Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotides. In: FISH Handbook for Biological Wastewater Treatment: Identification and quantification of microorganisms in activated sludge and biofilms by FISH. P.H. Nielsen; H. Daims; H. Lemmer (eds.) 1. ed. IWA Publishing Company, London, UK p. 73-84.

Nielsen, J.L., Kragelund, C. and Nielsen, P.H. (2009): Combination of Fluorescence in situ Hybridization with staining techniques for cell viability and accumulation of PHA and polyP in complex microbial system. Chapter 7 (p. 103-116) in "Bioremediation, Methods in Molecular Biology" (Ed. S. Gummings). The Humana Press Inc., New Jersey.

Nielsen, J.L., Kragelund, C. and Nielsen, P.H. (2009): Ecophysiological Analysis of Microorganisms in Complex Microbial Systems by Combination of Fluorescence In Situ Hybridization with Extracellular Staining Techniques. Chapter 8 (p. 117-128) in "Bioremediation, Methods in Molecular Biology" (Ed. S. Gummings). The Humana Press Inc., New Jersey.

Kragelund, C., Müller, E., Schade, M., Nguyen, H.T.T., Lemmer, H., Seviour, R. and Nielsen, P.H. (2009): Identification of filamentous bacteria by FISH. In: FISH Handbook for Biological Wastewater Treatment: Identification and quantification of microorganisms in activated sludge and biofilms by FISH. P.H. Nielsen; H. Daims; H. Lemmer (eds). 1. ed. IWA Publishing Company, London, UK p. 33-68.

Nielsen, P.H., Lemmer, H. and Daims, H. (2009): FISH Handbook of Wastewater Treatment. IWA Publishing Company, London, UK. Editors. ISBN: 9781843392316.

Nielsen, P.H., Lemmer, H. and Daims, H. (2009): Introduction. In: FISH Handbook for Biological Wastewater Treatment: Identification and quantification of microorganisms in activated sludge and biofilms by FISH. P.H. Nielsen; H. Daims; H. Lemmer (eds.) 1. ed. IWA Publishing Company, London, UK p. 1-8.

Nielsen, P.H., Nguyen, H.T.T., McIlroy, S.J., Mielczarek, A.T. and Seviour, R. (2009): Identification of polyphosphate-accumulating and glycogen-accumulating organisms by FISH. In: FISH Handbook for Biological Wastewater Treatment: Identification and quantification of microorganisms in activated sludge and biofilms by FISH. P.H. Nielsen; H. Daims; H. Lemmer (eds.). 1. ed. IWA Publishing Company, London, UK p. 25-32.

DANISH ARTICLES:

2016

Albertsen M., Kirkegaard R., Nielsen P.H. (2016): Comammox: Et nyt trin i kvælstofkredsløbet. Spildevandsteknisk Tidsskrift “Spildevand” 5 (16): 12-13.

Reitzel, K., P.H. Nielsen, L.B. Staal, M. Nierychlo, U.G. Nielsen C. Jørgensen (2016): Ny metode til måling af polyfosfat i spildevandsslam. Dansk Kemi 97(6/7): 24-27.

Kristensen, J.M., M. Nierychlo, M. Albertsen og P.H. Nielsen (2016): Bakterier i indløbsspildevand: Betyder de noget for bakteriesammensætningen på aktivt slam renseanlæg? Spildevandsteknisk Tidsskrift 44 (1): 25-27.

2015

Reitzel, K., P.H. Nielsen, M.L. Christensen, H.Qu, R. Wimmer, M. Nierychlo, C. Jørgensen,  U.G Nielsen (2015): ReCoverP – genvinding af fosfor fra spildevandsslam. Dansk Kemi 96(6/7): 25-27.

2014

Nielsen P.H., Albertsen M., Karst S., Kirkegaard R., Nierychlo M. (2014): Ny DNA-metode til analyse af bakterier giver helt nye muligheder. Spildevandsteknisk Tidsskrift 42(5): 37-39.

Nielsen P.H., Albertsen M., Karst S., Kirkegaard R., Nierychlo M. (2014): Kom slamprøver i fryseren. Spildevandsteknisk Tidsskrift 42(5): 40.

Hansen A.A. og Nielsen P.H. (2014): Nyt, dansk opslagsværk til spildevandsrensning. Spildevandsteknisk Tidsskrift 42(5): 41.

Hansen, A.A., V. Borregard, L. Nielsen,  P.H. Nielsen (2014): Dyk ned i en slamprøve og se, hvad det fortæller om processerne i et rensesanlæg. Spildevandsteknisk Tidsskrift, Spildevands Teknisk Forening 42(1): 44-45.

2012

Vangsgaard, A.K., Gernaey, K.V., Sin, G., Mutlu, A.G. & Smets, B.F. (2012): Energibesparende biologisk proces til kvælstoffjernelse i spildevand. Dansk Kemi 93(10): 16-18.

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