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
Fingerprint
- 1 Similar Profiles
Collaborations from the last five years
-
MicroFungi – Identify, map and explore the importance of soil fungal communities for soil health assessment and ecosystem quality across Denmark
Albertsen, M. (PI), Nielsen, P. H. (PI), Hugenholtz, P. (PI), Singleton, C. M. (PI), Sereika, M. (Project Participant), Chaumeil, P.-A. (Project Participant), Chuvochina, M. (Project Participant), Parks, D. (Project Participant), Rodriguez Rojas, M. (PI), Kale, V. (Project Participant), Normand, S. (PI), Greve, M. H. (PI) & Wollesen de Jonge, L. (PI)
01/09/2025 → 31/08/2028
Project: Research
-
CERO-MP: Cost Efficient Reduction of Micropollutants
Jørgensen, M. K. (PI), Nielsen, P. H. (CoI), Christensen, M. L. (CoI), Hove Hansen, S. (CoI) & Nielsen, M. H. (CoI)
01/01/2025 → 31/10/2027
Project: Research
-
Unlocking the Microbial Secrets of Biogas Reactors: From DNA Sequencing to Yield Maximization
Jiang, C. (PI), Nielsen, P. H. (Supervisor) & Singleton, C. M. (Supervisor)
01/06/2024 → 31/05/2026
Project: Research
-
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
-
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
Research output
-
Global insights into extracellular polymeric substances from activated sludge: Yield, composition, and microbial communities
De Bruin, S., Riisgaard-Jensen, M., Hansen, S. H., Van Loosdrecht, M. C. M., Nielsen, P. H. & Lin, Y., 15 Jan 2026, In: Water Research. 289, Pt A, 11 p., 124726.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile4 Link opens in a new tab Citations (Scopus)13 Downloads (Pure) -
Nanopore sequencing reaches amplicon sequence variant (ASV) resolution
Riisgaard-Jensen, M., Villanelo, S. A. R., Andersen, K. S., Kirkegaard, R., Hansen, S. H., Jiang, C., Stefansen, A. V., Thomsen, J. H. D., Nielsen, P. H. & Dueholm, M. K. D., 28 Feb 2026, bioRxiv, 18 p.Research output: Working paper/Preprint › Preprint
Open Access -
The Microflora Danica atlas of Danish environmental microbiomes
Singleton, C., Jensen, T., Delogu, F., Knudsen, K., Sørensen, E., Jørgensen, V., Karst, S., Yang, Y., Sereika, M., Petriglieri, F., Knutsson, S., Dall, S., Kirkegaard, R., Kristensen, J., Overgaard, C. K., Woodcroft, B., Speth, D., Aroney, S., The Microflora Danica Consortium & Pedersen, I. S. (Member of study group) & 17 others, , 22 Jan 2026, In: Nature. 649, 8098, p. 971–981 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile2 Link opens in a new tab Citations (Scopus)28 Downloads (Pure) -
A country-wide survey into the composition and transformation of short-chain organic acids in anaerobic sludge digesters at wastewater treatment plants in Denmark
Li, Z., Dueholm, M. K. D., Jiang, C., Zhu, B., Liu, L., Nielsen, P. H. & Hao, L., 11 Jul 2025, In: Scientific Reports. 15, 1, 12 p., 25001.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile1 Link opens in a new tab Citation (Scopus)25 Downloads (Pure) -
Assessing antimicrobial resistance connectivity across One Health sectors
Li, L., Li, B., Yin, X., Xia, Y., Yang, Y., Xu, X., Lam, T. T. Y., Leung, K. M. Y., Xu, F., Zhang, X., Guo, J., Schmitt, H., Wright, G. D., Midega, J., Bezuidenhout, C., Picão, R. C., Ahammad, S. Z., Smalla, K., Djordjevic, S. P. & Pruden, A. & 35 others, , Oct 2025, In: Nature Water. 3, 10, p. 1100-1113 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
6 Link opens in a new tab Citations (Scopus)
Datasets
-
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
-
MOESM5 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_d5.v1, https://figshare.com/articles/MOESM5_of_Diversity_of_microbial_carbohydrate-active_enzymes_in_Danish_anaerobic_digesters_fed_with_wastewater_treatment_sludge/5135956
Dataset
-
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://figshare.com/articles/MOESM3_of_Diversity_of_microbial_carbohydrate-active_enzymes_in_Danish_anaerobic_digesters_fed_with_wastewater_treatment_sludge/5135938
Dataset
-
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://figshare.com/articles/MOESM4_of_Diversity_of_microbial_carbohydrate-active_enzymes_in_Danish_anaerobic_digesters_fed_with_wastewater_treatment_sludge/5135947
Dataset
-
MOESM1 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_d1.v1, https://figshare.com/articles/MOESM1_of_Diversity_of_microbial_carbohydrate-active_enzymes_in_Danish_anaerobic_digesters_fed_with_wastewater_treatment_sludge/5135902
Dataset
Prizes
-
Clarivate Highly Cited Researchers
Nielsen, P. H. (Recipient), 2023
Prize: Research, education and innovation prizes
-
Clarivate Highly Cited Researchers
Nielsen, P. H. (Recipient), 2022
Prize: Research, education and innovation prizes
-
Ardern-Lockett Award, IWA/MEWE
Nielsen, P. H. (Recipient), 2021
Prize: Research, education and innovation prizes
-
Clarivate Highly Cited Researcher
Nielsen, P. H. (Recipient), 2021
Prize: Research, education and innovation prizes
-
Activities
-
MicroFlora Danica: Diversity, homogenisation, and the hidden nitrifiers of Denmark’s microbial atlas
Singleton, C. M. (Lecturer), Knudsen, K. S. (Lecturer), Jensen, T. B. N. (Lecturer), Speth, D. R. (Lecturer), Delogu, F. (Lecturer), Yang, Y. (Lecturer), Sereika, M. (Lecturer), Mølvang Dall, S. (Lecturer), Kirkegaard, R. H. (Lecturer), Kristensen, J. M. (Lecturer), Woodcroft, B. J. (Lecturer), Aroney, S. T. N. (Lecturer), Dueholm, M. K. D. (Lecturer), Wagner, M. (Lecturer), Nielsen, P. H. (Lecturer) & Albertsen, M. (Lecturer)
23 Jun 2025Activity: Talks and presentations › Conference presentations
-
Identifying and exploring epiphytic bacteria in wastewater treatment plants: unveiling their symbiotic role
Kondrotaite, Z. (Speaker), Petriglieri, F. (Other), Nierychlo, M. A. (Other), Jiang, C. (Other), Singleton, C. M. (Other) & Nielsen, P. H. (Other)
2025 → …Activity: Talks and presentations › Conference presentations
-
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
File -
Co-founder and partner of DNAsense ApS
Nielsen, P. H. (Consultant)
2014 → 2024Activity: Public/private sector consultancy and other employment › Starting your own company
-
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
Press/Media
-
Danmark får nyt atlas over naturens usynlige liv
Albertsen, M. & Nielsen, P. H.
17/02/2026
1 item of Media coverage
Press/Media: Press / Media
-
Storslået og betydningsfuldt: Ingeniøren kårer Danmarks mikroflora-kortlægning som årets største, danske videnskabelige bidrag
Nielsen, P. H. & Albertsen, M.
06/01/2026
1 item of Media coverage
Press/Media: Press / Media
-
AAU står bag årets største videnskabelige gennembrud i Danmark
Albertsen, M. & Nielsen, P. H.
25/12/2025 → 27/12/2025
4 items of Media coverage
Press/Media: Press / Media
-
Storslået og betydningsfuldt: Danmarks mikroflora-kortlægning vækker international opsigt
Nielsen, P. H. & Albertsen, M.
19/12/2025
3 items of Media coverage
Press/Media: Press / Media
-
Dansk forskningsgennembrud kortlægger usynligt liv i naturen
Albertsen, M. & Nielsen, P. H.
08/12/2025 → 09/12/2025
3 items of Media coverage
Press/Media: Press / Media
Impacts
-
Knowledge of microorganisms connecting culture and sustainability
Albertsen, M. (Participant) & Nielsen, P. H. (Participant)
Impact: Green impact, Cultural impact, Other impact