Projects per year
Personal profile
Research profile
Our main interest is microbial consortia and to understand how they control the function of environmental and engineered systems. We study microbial diversity and functional traits from species to ecosystems including factors controlling community assembly and dynamics. We apply a range of complementary approaches from DNA-based community surveys, (meta)genomics, metabolic reconstruction, to the use of isotopes, confocal microscopy, and Raman microspectroscopy. Main focus areas:
- Microbial communities and key processes in wastewater treatment plants and resource recovery systems (MiDAS)
- Microbial extracellular biopolymers as recycled resources (REThiNk)
- Novel microbes, functions and biogeography in natural and engineered ecosystems (Microflora Danica)
Teaching profile
Course responsible for Environmental Biotechnology which is a 5 ECTS semester course for 7th-semester students on Biotechnology, Biology and Chemistry. Supervising semester group projects (15 ETCS) on 7th-semester Biotechnology within the theme Molecular Methods.
Keywords
- Environment
- Mikrobial communities (biofilm and consortia)
- Identification and characterization of culture-independent bacteria
- Adhesion of bacteria to surfaces, exopolymers
- Biological treatment of wastewater, drinking water and air
- Production of bioenergy (biogas), recovery of resources (phosphate)
- Development of new methods in microbial ecology (-omics methods, isotopes, single cell techniques)
- Biomedical Engineering
- Disease-causing Bacteria and Implants
- Chemistry and Bioscience
- Environmental biotechnology
- Microbiology
- Microbial communities
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Collaborations from the last five years
Dive into details by clicking on the dots.
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AAU Water
Lykke, A. (Project Coordinator), Quist-Jensen, C. A. (PI), Vollertsen, J. (PI), Nielsen, P. H. (PI), Larsen, K. G. (PI), Ali, A. (PI), Aschmoneit, F. J. (PI), Pomianowski, M. Z. (PI) & Wisniewski, R. (PI)
01/05/2024 → …
Project: Research
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CERO-MP: Cost Efficient Reduction of Micropollutants
Jørgensen, M. K. (PI), Nielsen, P. H. (CoI) & Christensen, M. L. (CoI)
01/01/2023 → 31/10/2025
Project: Research
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REThiNk: Recovery of extracellular polymers from wastewater treatment residuals as a new circular biopolymer (REThiNk)
Nielsen, P. H. (PI), Dueholm, M. K. D. (PI), Seviour, T. (PI), Van Loosdrecht, M. C. M. (PI), Hove Hansen, S. (Project Coordinator), Riisgaard-Jensen, M. (Project Participant), Vestergaard, S. Z. (Project Participant), Liu, L. (Project Participant), Daugberg, A. (Project Participant) & Nierychlo, M. A. (Project Participant)
Otto Mønsteds Fond, Novo Nordisk Foundation, International Water Association Denmark
01/09/2022 → 31/08/2027
Project: Research
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MiDAS Sweden: The microbial database for Swedish wastewater treatment plants and digesters
Nielsen, P. H. (PI), Hove Hansen, S. (Project Coordinator), Nierychlo, M. A. (Project Participant), Petersen, A.-K. C. (Project Participant) & Andersen, K. S. (Project Participant)
01/07/2020 → …
Project: Research
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Microflora Danica: The Microbiome of Denmark
Albertsen, M. (PI), Nielsen, P. H. (PI), Jensen, T. B. N. (Project Participant), Sørensen, E. A. (Project Participant), Sereika, M. (Project Participant), Dottorini, G. (Project Participant), Petriglieri, F. (Project Participant), Jørgensen, V. R. (Project Participant), Kirkegaard, R. H. (Project Participant), Yang, Y. (Project Participant), Karst, S. M. (Project Participant), Giguere, A. T. (Project Participant), Knutsson, S. (Project Participant), Singleton, C. M. (Project Participant), Dueholm, M. K. D. (Project Participant), Mølvang Dall, S. (Project Participant), Kristensen, J. M. (Project Participant) & Delogu, F. (Project Participant)
01/01/2019 → 31/12/2025
Project: Research
Research output
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Biokinetic soft-sensing using Thiothrix and Ca. Microthrix bacteria to calibrate secondary settling, aeration and N2O emission digital twins
Bakos, V., Qiu, Y., Nierychlo, M., Nielsen, P. H. & Plósz, B. G., 1 May 2025, In: Water Research. 275, 16 p., 123164.Research output: Contribution to journal › Journal article › Research › peer-review
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Diversity and abundance of filamentous and non-filamentous “Leptothrix” in global wastewater treatment plants
Suazo, K. S., Nierychlo, M., Kondrotaite, Z., Petriglieri, F., Peces, M., Singleton, C., Dries, J. & Nielsen, P. H., 19 Mar 2025, In: Applied and Environmental Microbiology. 91, 3, 17 p., e01485-24.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile9 Downloads (Pure) -
Diversity and physiology of abundant Rhodoferax species in global wastewater treatment systems
Petersen, J. F., Valk, L. C., Verhoeven, M. D., Nierychlo, M. A., Singleton, C. M., Dueholm, M. K. D. & Nielsen, P. H., Jan 2025, In: Systematic and Applied Microbiology. 48, 1, 14 p., 126574.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile2 Citations (Scopus)6 Downloads (Pure) -
Fluorescently probing anaerobic digester sludge: Measuring single-cell anabolic activity in methanogens (Methanosarcina and Methanothermobacter) with deuterium-labeled Raman analysis
Fernando, E., Nielsen, P. H. & Nielsen, J. L., 5 Feb 2025, In: Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 326, 7 p., 125231.Research output: Contribution to journal › Journal article › Research › peer-review
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Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems
Zhu, C., Wu, L., Ning, D., Tian, R., Gao, S., Zhang, B., Zhao, J., Zhang, Y., Xiao, N., Wang, Y., Brown, M. R., Tu, Q., Global Water Microbiome Consortium, Ju, F., Wells, G. F., Guo, J., He, Z., Nielsen, P. H., Wang, A. & Zhang, Y. & 13 others, , 29 Apr 2025, In: Nature Communications. 16, 14 p., 4006.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile1 Citation (Scopus)4 Downloads (Pure)
Datasets
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Additional file 1 of Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants
Hu, H. (Creator), Kristensen, J. M. (Creator), Herbold, C. W. (Creator), Pjevac, P. (Creator), Kitzinger, K. (Creator), Hausmann, B. (Creator), Dueholm, M. K. D. (Creator), Nielsen, P. H. (Creator) & Wagner, M. (Creator), Figshare, 15 Aug 2024
DOI: 10.6084/m9.figshare.26694255, https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Global_abundance_patterns_diversity_and_ecology_of_Patescibacteria_in_wastewater_treatment_plants/26694255
Dataset
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Additional file 1 of Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants
Hu, H. (Creator), Kristensen, J. M. (Creator), Herbold, C. W. (Creator), Pjevac, P. (Creator), Kitzinger, K. (Creator), Hausmann, B. (Creator), Dueholm, M. K. D. (Creator), Nielsen, P. H. (Creator) & Wagner, M. (Creator), Figshare, 15 Aug 2024
DOI: 10.6084/m9.figshare.26694255.v1, https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Global_abundance_patterns_diversity_and_ecology_of_Patescibacteria_in_wastewater_treatment_plants/26694255/1
Dataset
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MOESM4 of Diversity of microbial carbohydrate-active enzymes in Danish anaerobic digesters fed with wastewater treatment sludge
Wilkens, C. (Creator), Busk, P. K. (Creator), Pilgaard, B. (Creator), Zhang, W.-J. (Creator), Nielsen, K. L. (Creator), Nielsen, P. H. (Creator) & Lange, L. (Creator), Figshare, 22 Jun 2017
DOI: 10.6084/m9.figshare.c.3808579_d4.v1, https://springernature.figshare.com/articles/dataset/MOESM4_of_Diversity_of_microbial_carbohydrate-active_enzymes_in_Danish_anaerobic_digesters_fed_with_wastewater_treatment_sludge/5135947/1
Dataset
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MOESM3 of Diversity of microbial carbohydrate-active enzymes in Danish anaerobic digesters fed with wastewater treatment sludge
Wilkens, C. (Creator), Busk, P. K. (Creator), Pilgaard, B. (Creator), Zhang, W.-J. (Creator), Nielsen, K. L. (Creator), Nielsen, P. H. (Creator) & Lange, L. (Creator), Figshare, 22 Jun 2017
DOI: 10.6084/m9.figshare.c.3808579_d3.v1, https://springernature.figshare.com/articles/dataset/MOESM3_of_Diversity_of_microbial_carbohydrate-active_enzymes_in_Danish_anaerobic_digesters_fed_with_wastewater_treatment_sludge/5135938/1
Dataset
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MOESM2 of Diversity of microbial carbohydrate-active enzymes in Danish anaerobic digesters fed with wastewater treatment sludge
Wilkens, C. (Creator), Busk, P. K. (Creator), Pilgaard, B. (Creator), Zhang, W.-J. (Creator), Nielsen, K. L. (Creator), Nielsen, P. H. (Creator) & Lange, L. (Creator), Figshare, 22 Jun 2017
DOI: 10.6084/m9.figshare.c.3808579_d2.v1, https://springernature.figshare.com/articles/dataset/MOESM2_of_Diversity_of_microbial_carbohydrate-active_enzymes_in_Danish_anaerobic_digesters_fed_with_wastewater_treatment_sludge/5135923/1
Dataset
Prizes
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Clarivate Highly Cited Researchers
Nielsen, P. H. (Recipient), 2023
Prize: Research, education and innovation prizes
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Clarivate Highly Cited Researchers
Nielsen, P. H. (Recipient), 2022
Prize: Research, education and innovation prizes
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Ardern-Lockett Award, IWA/MEWE
Nielsen, P. H. (Recipient), 2021
Prize: Research, education and innovation prizes
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Clarivate Highly Cited Researcher
Nielsen, P. H. (Recipient), 2021
Prize: Research, education and innovation prizes
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Activities
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MAGnifying biogas production efficiency: high-quality metagenome-assembled genome recovery in anaerobic digesters reveals abundant novel populations with key functional roles
Singleton, C. M. (Speaker), Jiang, C. (Other), Liu, L. (Other), Kirkegaard, R. H. (Other), Dueholm, M. K. D. (Other) & Nielsen, P. H. (Other)
12 Sept 2023Activity: Talks and presentations › Conference presentations
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Co-founder and partner of DNAsense ApS
Nielsen, P. H. (Consultant)
2014 → 2024Activity: Public/private sector consultancy and other employment › Starting your own company
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Advances and applications of FISHtechnology: environmental, drinking water and foodstuff analysis
Nielsen, P. H. (Speaker)
10 Dec 2007 → 11 Dec 2007Activity: Talks and presentations › Talks and presentations in private or public companies
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Conference on "Water" (Vandmiljø), IDAmiljø
Nielsen, P. H. (Speaker)
6 Nov 2007 → 7 Nov 2007Activity: Talks and presentations › Talks and presentations in private or public companies
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Sustainable Processes and Products, Danish Biotechnological Society
Nielsen, P. H. (Speaker)
4 Oct 2007Activity: Talks and presentations › Talks and presentations in private or public companies
Press/Media
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Stor pris til forsker bag kortlægning af bakterier i spildevand og naturtyper
09/05/2025 → 14/05/2025
4 items of Media coverage
Press/Media: Press / Media
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Videnskabernes Selskabs hædrer et livsværk af mikroskopiske opdagelser med kæmpe betydning
25/04/2025 → 29/04/2025
2 items of Media coverage
Press/Media: Press / Media
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Overskydende biomasse i spildevand kan udnyttes på nye måder
29/04/2025
1 item of Media coverage
Press/Media: Press / Media
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Highlights fra Nordic Bioplastic Conference 2025
28/04/2025
1 item of Media coverage
Press/Media: Press / Media
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Vandsektorens faglige fætter/kusine-fest sætter suveræn deltagerrekord
11/12/2024
1 item of Media coverage
Press/Media: Press / Media