Journal Articles
Andersen, Martin H., McIlroy, Simon J., Nierychlo, Marta, Nielsen, Per H. and Albertsen, Mads (2018). Genomic insights into Candidatus Amarolinea aalborgensis gen. nov., sp. nov., associated with settleability problems in wastewater treatment plants. Systematic and Applied Microbiology, 42 (1), 77-84. doi: 10.1016/j.syapm.2018.08.001
Hao, Liping, McIlroy, Simon Jon, Kirkegaard, Rasmus Hansen, Karst, Søren Michael, Fernando, Warnakulasuriya Eustace Yrosh, Aslan, Hüsnü, Meyer, Rikke Louise, Albertsen, Mads, Nielsen, Per Halkjær and Dueholm, Morten Simonsen (2018). Novel prosthecate bacteria from the candidate phylum Acetothermia. The ISME Journal, 12 (9), 2225-2237. doi: 10.1038/s41396-018-0187-9
McIlroy, Simon J., Onetto, Cristobal A., McIlroy, Bianca, Herbst, Florian-Alexander, Dueholm, Morten S., Kirkegaard, Rasmus H., Fernando, Eustace, Karst, Soren M., Nierychlo, Marta, Kristensen, Jannie M., Eales, Kathryn L., Grbin, Paul R., Wimmer, Reinhard and Nielsen, Per Halkjaer (2018). Genomic and in situ analyses reveal the Micropruina spp. as abundant fermentative glycogen accumulating organisms in enhanced biological phosphorus removal systems. Frontiers in Microbiology, 9 (MAY) 1004, 1004. doi: 10.3389/fmicb.2018.01004
Jiang, Chenjing, Qi, Rong, Hao, Liping, McIlroy, Simon Jon and Nielsen, Per Halkjær (2018). Monitoring foaming potential in anaerobic digesters. Waste Management, 75, 280-288. doi: 10.1016/j.wasman.2018.02.021
Carvalho, Gilda, Pedras, Inês, Karst, Soren M., Oliveira, Catarina S. S., Duque, Anouk F., Nielsen, Per H. and Reis, Maria A. M. (2018). Functional redundancy ensures performance robustness in 3-stage PHA-producing mixed cultures under variable feed operation. New Biotechnology, 40, 207-217. doi: 10.1016/j.nbt.2017.08.007
Kirkegaard, Rasmus H., McIlroy, Simon J., Kristensen, Jannie M., Nierychlo, Marta, Karst, Soren M., Dueholm, Morten S., Albertsen, Mads and Nielsen, Per H. (2017). The impact of immigration on microbial community composition in full-scale anaerobic digesters. Scientific Reports, 7 (1) 9343, 9343. doi: 10.1038/s41598-017-09303-0
Mcllroy, Simon J., Kirkegaard, Rasmus H., Dueholm, Morten S., Fernando, Eustace, Karst, Soren M., Albertsen, Mads and Nielsen, Per H. (2017). Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge. Frontiers in Microbiology, 8 (JUN) 1134. doi: 10.3389/fmicb.2017.01134
McIlroy, Simon Jon, Kirkegaard, Rasmus Hansen, McIlroy, Bianca, Nierychlo, Marta, Kristensen, Jannie Munk, Karst, Soren Michael, Albertsen, Mads and Nielsen, Per Halkjaer (2017). MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups. Database, 2017 (1). doi: 10.1093/database/bax016
Silva, Ana F., Antunes, Sílvia, Saunders, Aaron, Freitas, Filomena, Vieira, Anabela, Galinha, Claudia F., Nielsen, Per H., Barreto Crespo, Maria Teresa and Carvalho, Gilda (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 (19), 8507-8521. doi: 10.1007/s00253-016-7617-2
Kirkegaard, Rasmus Hansen, Dueholm, Morten Simonsen, McIlroy, Simon Jon, Nierychlo, Marta, Karst, Soren Michael, Albertsen, Mads and Nielsen, Per Halkjaer (2016). Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters. ISME Journal, 10 (10), 2352-2364. doi: 10.1038/ismej.2016.43
McIlroy, Simon Jon, Karst, Soren Michael, Nierychlo, Marta, Dueholm, Morten Simonsen, Albertsen, Mads, Kirkegaard, Rasmus Hansen, Seviour, Robert James and Nielsen, Per Halkjaer (2016). Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge. ISME Journal, 10 (9), 2223-2234. doi: 10.1038/ismej.2016.14
Albertsen, Mads, McIlroy, Simon J., Stokholm-Bjerregaard, Mikkel, Karst, Søren M. and Nielsen, Per H. (2016). "Candidatus Propionivibrio aalborgensis": a novel glycogen accumulating organism abundant in full-scale enhanced biological phosphorus removal plants. Frontiers in Microbiology, 7 (JUL) 1033, 1033. doi: 10.3389/fmicb.2016.01033
McIlroy, Simon Jon, Awata, Takanori, Nierychlo, Marta, Albertsen, Mads, Kindaichi, Tomonori and Nielsen, Per Halkjaer (2015). Characterization of the in situ ecophysiology of novel phylotypes in nutrient removal activated sludge treatment plants. PloS One, 10 (9) e0136424, e0136424. doi: 10.1371/journal.pone.0136424
McIlroy, Simon J., Albertsen, Mads, Andresen, Eva K., Saunders, Aaron M., Kristiansen, Rikke, Stokholm-Bjerregaard, Mikkel, Nielsen, Kare L. and Nielsen, Per H. (2014). 'Candidatus Competibacter'-lineage genomes retrieved from metagenomes reveal functional metabolic diversity. ISME Journal, 8 (3), 613-624. doi: 10.1038/ismej.2013.162
McIlroy, Simon Jon, Kristiansen, Rikke, Albertsen, Mads, Karst, Soren Michael, Rossetti, Simona, Nielsen, Jeppe Lund, Tandoi, Valter, Seviour, Robert James and Nielsen, Per Halkjaer (2013). Metabolic model for the filamentous 'Candidatus Microthrix parvicella' based on genomic and metagenomic analyses. ISME Journal, 7 (6), 1161-1172. doi: 10.1038/ismej.2013.6
Albertsen, Mads, Hugenholtz, Philip, Skarshewski, Adam, Nielsen, Kare L., Tyson, Gene W. and Nielsen, Per H. (2013). Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology, 31 (6), 533-538+. doi: 10.1038/nbt.2579
Kristiansen, Rikke, Hien Thi Thu Nguyen, Saunders, Aaron Marc, Nielsen, Jeppe Lund, Wimmer, Reinhard, Vang Quy Le, McIlroy, Simon Jon, Petrovski, Steve, Seviour, Robert J., Calteau, Alexandra, Nielsen, Kare Lehmann and Nielsen, Per Halkjaer (2013). A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal. ISME Journal, 7 (3), 543-554. doi: 10.1038/ismej.2012.136
Albuquerque, Maria G. E., Carvalho, Gilda, Kragelund, Caroline, Silva, Ana F., Barreto Crespo, Maria T., Reis, Maria A. M. and Nielsen, Per H. (2013). Link between microbial composition and carbon substrate-uptake preferences in a PHA-storing community. ISME Journal, 7 (1), 1-12. doi: 10.1038/ismej.2012.74
Conference Papers
Burow, L. C., Kong, Y., Nielsen, L., Blackall, L. L. and Nielsen, P. H. (2006). Occurrence and ecophysiology of uncultured defluvicoccus vanus-related organisms in full-scale enhanced biological phosphorus removal wastewater treatment plants. 11th International Symposium on Microbial Ecology - ISME 11, Vienna, Austria, 20-25 August 2006. Switzerland: Kenes International.
Tykesson, E., Blackall, L. L., Kong, Y, Nielsen, P Halkjaer and la Cour Jansen, J. (2005). Applicability of experience from laboratory reactors with biological phosphorus removal in full-scale plants. 4th IWA ASPD Specialist Conference - Microbial Population Dyn, Gold Coast, QLD, Australia, 17-20 July 2005. Brisbane, Qld, Australia: AWMC.
Aquino de Muro, M., Blackall, L. L., Nielson, J. L. and Nielsen, P. H. (1999). Phylogenetic and nutritional differences detected by MAR and FISH among coexisting strains of Thiothrix and Type 021N in activated sludge. IXth International Congress of Bacteriology and Applied Micry, Sydney, NSW, 16-20 August 1999. not available: not available.
Nielsen, P. H., Andreasen, K., Wagner, M., Blackall, L. L., Lemmer, H. and Seviour, R. J. (1998). Variability of type 021N in activated sludge as determined by in situ substrate uptake pattern and in situ hybridization with fluorescent rRNA targeted probes. Proceedings of the 1997 2nd International Conference on Microorganisms in Activated Sludge and Biofilm Processes, , , July 21, 1997-July 23, 1997. Elsevier Sci Ltd. doi: 10.1016/S0273-1223(98)00170-X