Publications

MiDAS:

McIlroy, S.J., Kirkegaard, R.H., McIlroy, B., Nierychlo, M., Kristensen, J.M., Karst, S.M., Albertsen, M., Nielsen, P.H., 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. doi:10.1093/database/bax016

McIlroy, S.J., Saunders, A.M., Albertsen, M., Nierychlo, M., McIlroy, B., Hansen, A.A., Karst, S.M., Nielsen, J.L. and Nielsen, P.H. (2015) MiDAS: the field guide to the microbes of activated sludge. Database, Vol. 2015, Article ID bav062; doi:10.1093/database/bav062.


Read more about our conceptual model of the activated sludge ecosystem:

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

Albertsen M., Karst S.M., Ziegler A.S., Kirkegaard R.H., Nielsen P.H. (2015) Back to basics – the influence of DNA extraction and primer choice on phylogenetic analysis in activated sludge communities. PLOS ONE, doi: 10.1371/journal.pone.0132783.

Nielsen, P.H., Saunders, A.M., Hansen, A.A., Larsen, P., & Nielsen, J.L. (2012). Microbial communities involved in enhanced biological phosphorus removal from wastewater - a model system in environmental biotechnology. Current Opinion in Biotechnology, 23(3), 452–459.

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

 

Examples of articles citing and using MiDAS:

(2018)

Bonk, F., D Popp, H Harms, F Centler (2018): PCR-based quantification of taxa-specific abundances in microbial communities: Quantifying and avoiding common pitfalls. J Microbiol Methods, 153, 139-147.

Bonk, F., Popp, D., Weinrich, S., Sträuber, H., Kleinsteuber, S., Harms, H., Centler, F., (2018): Intermittent fasting for microbes: how discontinuous feeding increases functional stability in anaerobic digestion. Biotechnology for Biofuels 11, 274. https://doi.org/10.1186/s13068-018-1279-5

Fang, D., Zhao, G., Xu, X., Zhang, Q., Shen, Q., Fang, Z., Huang, L., Ji, F., (2018): Microbial community structures and functions of wastewater treatment systems in plateau and cold regions. Bioresource Technology 249, 684–693. https://doi.org/10.1016/j.biortech.2017.10.063

Gonzalez-Martinez, A., Sihvonen, M., Muñoz-Palazon, B., Rodriguez-Sanchez, A., Mikola, A., Vahala, R., (2018): Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea , Bacteria and Fungi. Scientific Reports 8, 2208. https://doi.org/10.1038/s41598-018-20633-5

Günther, S.,  D Becker, T Hübschmann, S Reinert, S Kleinsteuber, S Müller, C Wilhelm (2018): Long-Term Biogas Production from Glycolate by Diverse and Highly Dynamic Communities. Microorganisms, 6, 103; doi:10.3390/microorganisms6040103.

Jiang, X.-T., Ye, L., Ju, F., Li, B., Ma, L.-P., Zhang, T., (201): Temporal dynamics of activated sludge bacterial communities in two diversity variant full-scale sewage treatment plants. Applied Microbiology and Biotechnology 102, 9379–9388. https://doi.org/10.1007/s00253-018-9287-8

(2017)

Cokro, AA, Y Law, RBH Williams, Y Cao, PH Nielsen, S Wuertz (2017): Non-denitrifying polyphosphate accumulating organisms obviate requirement for anaerobic condition. Water Research 111, 393–403. doi:10.1016/j.watres.2017.01.006

Keene, N.A., Reusser, S.R., Scarborough, M.J., Grooms, A.L., Seib, M., Santo Domingo, J., Noguera, D.R., 2017. Pilot plant demonstration of stable and efficient high rate biological nutrient removal with low dissolved oxygen conditions. Water Research 121, 72–85. https://doi.org/10.1016/j.watres.2017.05.029

Rubio-Rincón, F.J., Welles, L., Lopez-Vazquez, C.M., Nierychlo, M., Abbas, B., Geleijnse, M., Nielsen, P.H., van Loosdrecht, M.C.M., Brdjanovic, D., (2017): Long-term effects of sulphide on the enhanced biological removal of phosphorus: The symbiotic role of Thiothrix caldifontis. Water Research 116, 53–64. https://doi.org/10.1016/j.watres.2017.03.017

Stokholm-Bjerregaard, M., McIlroy, S.J., Nierychlo, M., Karst, S.M., Albertsen, M., Nielsen, P.H., (2017): A Critical Assessment of the Microorganisms Proposed to be Important to Enhanced Biological Phosphorus Removal in Full-Scale Wastewater Treatment Systems. Front. Microbiol. 8. doi.org/10.3389/fmicb.2017.00718

Szabó, E., R Liébana, M Hermansson, O Modin, F Persson, and B-M Wilén (2017): Microbial Population Dynamics and Ecosystem Functions of Anoxic/Aerobic Granular Sludge in Sequencing Batch Reactors Operated at Different Organic Loading Rates. Frontiers in Microbiology 8. doi:10.3389/fmicb.2017.00770

(2016)

Laureni, M., Falås, P., Robin, O., Wick, A., Weissbrodt, D.G., Nielsen, J.L., Ternes, T.A., Morgenroth, E., Joss, A., 2016. Mainstream partial nitritation and anammox: long-term process stability and effluent quality at low temperatures. Water Research 101, 628–639. https://doi.org/10.1016/j.watres.2016.05.005

 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.

Silva, A.F., Antunes, S., Saunders, A., Freitas, F., Vieira, A., Galinha, C.F., Nielsen, P.H., Crespo, M.T.B., Carvalho, G., 2016. Impact of sludge retention time on the fine composition of the microbial community and extracellular polymeric substances in a membrane bioreactor. Appl Microbiol Biotechnol 100, 8507–8521. https://doi.org/10.1007/s00253-016-7617-2

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.

(2015)

McIlroy, S.J., Awata, T., Nierychlo, M., Albertsen, M., Kindaichi, T., Nielsen, P.H., (2015): Characterization of the In Situ Ecophysiology of Novel Phylotypes in Nutrient Removal Activated Sludge Treatment Plants. PLOS ONE 10, e0136424. https://doi.org/10.1371/journal.pone.0136424

to see full citation list, please click here (McIlroy et al., 2015) and here (McIlroy et al., 2017). 

  

Slideshows:

DNA extraction and primer selection for Activated Sludge

MEWE 2013 workshop by Søren M. Karst (Aalborg University, Denmark).

 

The importance of a curated 16S database

MEWE 2013 workshop by Aaron M. Saunders (Aalborg University, Denmark).


Contact us at mail@midasfieldguide.org