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List of works by Per Halkjær Nielsen

"Candidatus Dechloromonas phosphoritropha" and "Ca. D. phosphorivorans", novel polyphosphate accumulating organisms abundant in wastewater treatment systems

scientific article published on 21 June 2021

"Candidatus Propionivibrio aalborgensis": A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants

scientific article published on 04 July 2016

"Microthrix parvicella", a filamentous bacterium causing bulking and foaming in activated sludge systems: a review of current knowledge

scientific article

'Candidatus Competibacter'-lineage genomes retrieved from metagenomes reveal functional metabolic diversity.

scientific article published on 31 October 2013

A Critical Assessment of the Microorganisms Proposed to be Important to Enhanced Biological Phosphorus Removal in Full-Scale Wastewater Treatment Systems

scientific article

A conceptual ecosystem model of microbial communities in enhanced biological phosphorus removal plants.

scientific article

A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal.

scientific article

A new class of hybrid secretion system is employed in Pseudomonas amyloid biogenesis

scientific article published on 15 August 2017

Abundance and ecophysiology of Defluviicoccus spp., glycogen-accumulating organisms in full-scale wastewater treatment processes

scientific article

Abundance and phylogenetic affiliation of iron reducers in activated sludge as assessed by fluorescence in situ hybridization and microautoradiography

scientific article

Activity and identity of fermenting microorganisms in full-scale biological nutrient removing wastewater treatment plants

scientific article published on 28 June 2008

Adhesion characteristics of nitrifying bacteria in activated sludge.

scientific article published on 29 February 2008

Ammonia and temperature determine potential clustering in the anaerobic digestion microbiome

scientific article published on 25 February 2015

Amyloid adhesins are abundant in natural biofilms

scientific article

Amyloid-like adhesins produced by floc-forming and filamentous bacteria in activated sludge

scientific article

Author Correction: Global diversity and biogeography of bacterial communities in wastewater treatment plants

scientific article published on 01 December 2019

Back to Basics--The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities.

scientific article published on 16 July 2015

Bacterial diversity in suspected prosthetic joint infections: an exploratory study using 16S rRNA gene analysis.

scientific article

Biocorrosion and biofilm formation in a nutrient limited heating system subjected to alternating microaerophilic conditions

scientific article published in November 2009

Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities

scientific article

Butyric acid- and dimethyl disulfide-assimilating microorganisms in a biofilter treating air emissions from a livestock facility

scientific article

Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta

scientific article published on 25 July 2019

Characterization of activated sludge flocs by confocal laser scanning microscopy and image analysis

scientific article

Characterization of the In Situ Ecophysiology of Novel Phylotypes in Nutrient Removal Activated Sludge Treatment Plants

scientific article published on 4 September 2015

Characterization of the loosely attached fraction of activated sludge bacteria

scientific article published on 7 September 2007

Cohn's Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase

scholarly article

Combination of fluorescence in situ hybridization with staining techniques for cell viability and accumulation of PHA and polyP in microorganisms in complex microbial systems

scientific article published on 01 January 2010

Community structure of bacteria and fungi in aerosols of a pig confinement building.

scientific article

Comparison of nutrient-removing microbial communities in activated sludge from full-scale MBRs and conventional plants.

scientific article published in January 2013

Comparison of targeted peptide quantification assays for reductive dehalogenases by selective reaction monitoring (SRM) and precursor reaction monitoring (PRM).

scientific article published on 13 November 2013

Complete Genome Sequence of Actinobaculum schaalii Strain CCUG 27420.

scientific article published on 4 September 2014

Complete Genome Sequence of Pseudomonas sp. UK4, a Model Organism for Studies of Functional Amyloids in Pseudomonas

scientific article published on 11 September 2014

Complete Genome Sequence of the Bacterium Aalborg_AAW-1, Representing a Novel Family within the Candidate Phylum SR1.

scientific article published on 11 June 2015

Complete nitrification by Nitrospira bacteria

scientific article

Complete nitrification by a single microorganism

scientific article

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

scientific article published on 31 March 2021

Correction: Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system

scientific article published on 10 July 2020

Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system

scientific article

Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge

scientific article

Curli Functional Amyloid Systems Are Phylogenetically Widespread and Display Large Diversity in Operon and Protein Structure ⬇️

scientific article published on December 12, 2012

Degradation of phthalate esters in an activated sludge wastewater treatment plant

scientific article published on 26 January 2007

Denitrification activity of polyphosphate accumulating organisms (PAOs) in full-scale wastewater treatment plants

scientific article published on 01 December 2018

Detection of Pathogenic Biofilms with Bacterial Amyloid Targeting Fluorescent Probe, CDy11.

scientific article published on 18 December 2015

Detection of activity among uncultured Actinobacteria in a drinking water reservoir

scientific article published in March 2006

Detection of microbial diversity in endocarditis using cultivation-independent molecular techniques

scientific article

Dewatering in biological wastewater treatment: A review.

scientific article published on 26 April 2015

Direct Identification of Functional Amyloid Proteins by Label-Free Quantitative Mass Spectrometry

scientific article published on 04 August 2017

Dynamics of the Fouling Layer Microbial Community in a Membrane Bioreactor.

scientific article

Ecophysiological analysis of microorganisms in complex microbial systems by combination of fluorescence in situ hybridization with extracellular staining techniques

scientific article published on 01 January 2010

Ecophysiology of a group of uncultured Gammaproteobacterial glycogen-accumulating organisms in full-scale enhanced biological phosphorus removal wastewater treatment plants

scientific article published in March 2006

Ecophysiology of abundant denitrifying bacteria in activated sludge.

scientific article published on 28 March 2007

Ecophysiology of different filamentous Alphaproteobacteria in industrial wastewater treatment plants

scientific article

Ecophysiology of mycolic acid-containing Actinobacteria (Mycolata) in activated sludge foams.

scientific article published on 27 April 2007

Ecophysiology of the Actinobacteria in activated sludge systems

scientific article published on 26 February 2008

Ecophysiology of the filamentous Alphaproteobacterium Meganema perideroedes in activated sludge

scientific article published in September 2005

Editorial: Microbial ecology

scientific article

Eikelboom's morphotype 0803 in activated sludge belongs to the genus Caldilinea in the phylum Chloroflexi

scientific article published on 14 March 2011

Enhancing metaproteomics--The value of models and defined environmental microbial systems

scientific article published in December 2015

Enumeration of acetate-consuming bacteria by microautoradiography under oxygen and nitrate respiring conditions in activated sludge

scientific article published in January 2002

Evaluation of the redox dye 5-cyano-2,3-tolyl-tetrazolium chloride for activity studies by simultaneous use of microautoradiography and fluorescence in situ hybridization

scientific article

Evolutionary insight into the functional amyloids of the pseudomonads

scientific article

Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira

scientific article

Experimental methods and modeling techniques for description of cell population heterogeneity.

scientific article published on 19 April 2011

Exploring the microbial influence on seasonal nitrous oxide concentration in a full-scale wastewater treatment plant using metagenome assembled genomes

scientific article published in 2022

Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira

scientific article published on 24 July 2020

Expression of Fap amyloids in Pseudomonas aeruginosa, P. fluorescens, and P. putida results in aggregation and increased biofilm formation

scientific article

Extracellular DNA is abundant and important for microcolony strength in mixed microbial biofilms

scientific article published on 30 November 2010

Fibrillation of the major curli subunit CsgA under a wide range of conditions implies a robust design of aggregation

scientific article published on 12 September 2011

Filtration properties of activated sludge in municipal MBR wastewater treatment plants are related to microbial community structure.

scientific article published on 12 September 2013

Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities

scientific article published on 02 September 2020

Functional amyloid in Pseudomonas

scientific article

Functional amyloids keep quorum-sensing molecules in check

scientific article

Functional bacterial amyloid increases Pseudomonas biofilm hydrophobicity and stiffness.

scientific article published on 7 October 2015

Functional redundancy ensures performance robustness in 3-stage PHA-producing mixed cultures under variable feed operation.

scientific article published on 21 August 2017

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

scientific article

Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge

scientific article published on 23 February 2016

Genomic insights into Candidatus Amarolinea aalborgensis gen. nov., sp. nov., associated with settleability problems in wastewater treatment plants

scientific article published on 16 August 2018

Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters

scientific article

Global diversity and biogeography of bacterial communities in wastewater treatment plants

scientific article published on 13 May 2019

Gravity drainage of activated sludge: new experimental method and considerations of settling velocity, specific cake resistance and cake compressibility.

scientific article

Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation

scientific article published in August 2014

High and stable substrate specificities of microorganisms in enhanced biological phosphorus removal plants

scientific article published on 16 January 2013

High diversity and abundance of putative polyphosphate-accumulating Tetrasphaera-related bacteria in activated sludge systems ⬇️

scientific article published on February 14, 2011

High quality draft genome sequence of Meganema perideroedes str. Gr1(T) and a proposal for its reclassification to the family Meganemaceae fam. nov

scientific article published on 27 February 2015

Identification and ecophysiological characterization of epiphytic protein-hydrolyzing saprospiraceae ("Candidatus Epiflobacter" spp.) in activated sludge

scientific article

Identification of active denitrifiers in full-scale nutrient removal wastewater treatment systems

scientific article

Identification of glucose-fermenting bacteria in a full-scale enhanced biological phosphorus removal plant by stable isotope probing

scientific article

Identity and ecophysiology of filamentous bacteria in activated sludge

scientific article published on 22 May 2009

Identity and ecophysiology of uncultured actinobacterial polyphosphate-accumulating organisms in full-scale enhanced biological phosphorus removal plants

scientific article published in July 2005

Identity, abundance and ecophysiology of filamentous Chloroflexi species present in activated sludge treatment plants

scientific article published in March 2007

Identity, abundance and ecophysiology of filamentous bacteria belonging to the Bacteroidetes present in activated sludge plants

scientific article

Impact of sludge retention time on the fine composition of the microbial community and extracellular polymeric substances in a membrane bioreactor

scientific article

In situ detection of protein-hydrolysing microorganisms in activated sludge

scientific article

In situ detection of starch-hydrolyzing microorganisms in activated sludge

scientific article published on 27 August 2008

In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth

scientific article published in July 2002

In situ substrate conversion and assimilation by nitrifying bacteria in a model biofilm

scientific article published on 01 September 2005

Influence of shear on nitrification rates in a membrane bioreactor

scientific article published in January 2014

Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions

scientific article

Intracellular Accumulation of Glycine in Polyphosphate-Accumulating Organisms in Activated Sludge, a Novel Storage Mechanism under Dynamic Anaerobic-Aerobic Conditions.

scientific article

Irreversible fouling of membrane bioreactors due to formation of a non-biofilm gel layer

scientific article published in January 2014

Isotope array analysis of Rhodocyclales uncovers functional redundancy and versatility in an activated sludge

scientific article published on 2 July 2009

Isotope labeling and microautoradiography of active heterotrophic bacteria on the basis of assimilation of 14CO(2).

scientific article

Label-free quantification reveals major proteomic changes in Pseudomonas putida F1 during the exponential growth phase

scientific article published on 29 June 2015

Limited dissemination of the wastewater treatment plant core resistome.

scientific article

Link between microbial composition and carbon substrate-uptake preferences in a PHA-storing community. ⬇️

scientific article

Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays

scientific article

Lipase and protease extraction from activated sludge

scientific article published in September 2003

Low temperature partial nitritation/anammox in a moving bed biofilm reactor treating low strength wastewater.

scientific article published on 16 July 2014

Major proteomic changes associated with amyloid-induced biofilm formation in Pseudomonas aeruginosa PAO1.

scientific article published on 31 October 2014

Mass-immigration determines the assembly of activated sludge microbial communities

scientific article published in 2021

Meganema perideroedes gen. nov., sp. nov., a filamentous alphaproteobacterium from activated sludge

scientific article

Metabolic Traits of Candidatus Accumulibacter clade IIF Strain SCELSE-1 Using Amino Acids As Carbon Sources for Enhanced Biological Phosphorus Removal

scientific article published on 16 December 2019

Metabolic modelling of full-scale enhanced biological phosphorus removal sludge

scientific article

Metabolic versatility in full-scale wastewater treatment plants performing enhanced biological phosphorus removal.

scientific article

Metagenomes from deep Baltic Sea sediments reveal how past and present environmental conditions determine microbial community composition

scientific article published on 12 August 2017

Metagenomes obtained by 'deep sequencing' - what do they tell about the enhanced biological phosphorus removal communities?

scientific article

Metaproteomics: Evaluation of protein extraction from activated sludge

scientific article published on 02 October 2014

MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

scientific article published on 07 April 2022

MiDAS: the field guide to the microbes of activated sludge.

scientific article published on 27 June 2015

Microautoradiographic study of Rhodocyclus-related polyphosphate-accumulating bacteria in full-scale enhanced biological phosphorus removal plants

scientific article

Monitoring antibiotic resistance genes in wastewater environments: The challenges of filling a gap in the One-Health cycle

scientific article published in February 2022

Non-denitrifying polyphosphate accumulating organisms obviate requirement for anaerobic condition

scientific article published on 3 January 2017

Novel prosthecate bacteria from the candidate phylum Acetothermia

scientific article published on 08 June 2018

Novel syntrophic bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics

scientific article published on 02 January 2020

On the evolution and physiology of cable bacteria

scientific article published on 19 August 2019

Peatland Acidobacteria with a dissimilatory sulfur metabolism

scientific article published on 23 February 2018

Peatland Acidobacteria with a dissimilatory sulfur metabolism

article published in 2017

Phylogenetic Identification and Substrate Uptake Patterns of Sulfate-Reducing Bacteria Inhabiting an Oxic-Anoxic Sewer Biofilm Determined by Combining Microautoradiography and Fluorescent In Situ Hybridization ⬇️

scientific article published on January 1, 2002

Phylogeny, physiology and distribution of 'Candidatus Microthrix calida', a new Microthrix species isolated from industrial activated sludge wastewater treatment plants

scientific article

Polyphosphate-accumulating organisms in full-scale tropical wastewater treatment plants use diverse carbon sources

scientific article published on 09 November 2018

Population dynamics of filamentous bacteria in Danish wastewater treatment plants with nutrient removal

scientific article

Proteome profile and proteogenomics of the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 grown on hexachlorobenzene as electron acceptor

scientific article

Quantification of cell-specific substrate uptake by probe-defined bacteria under in situ conditions by microautoradiography and fluorescence in situ hybridization

scientific article published in March 2003

Quantification of lipids and protein in thin biofilms by fluorescence staining

scientific article published in January 2008

Quenching effects in the application of multi-channel fluorescence in activated sludge suspended solids

scientific article published on 5 February 2008

Re-appraisal of the phylogeny and fluorescence in situ hybridization probes for the analysis of the Competibacteraceae in wastewater treatment systems

scientific article published on 2 December 2014

Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus “ Candidatus Accumulibacter” ⬇️

scientific article published on 25 April 2022

Resolving the individual contribution of key microbial populations to enhanced biological phosphorus removal with Raman-FISH

scientific article published on 20 March 2019

Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias.

scientific article published in January 2018

Sludge quality aspects of full-scale reed bed drainage

scientific article

Structure and function of the microbial community in a full-scale enhanced biological phosphorus removal plant

scientific article published in December 2007

Substrate-dependent denitrification of abundant probe-defined denitrifying bacteria in activated sludge

scientific article published on 22 September 2008

Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers

scientific article

The Proteome of Tetrasphaera elongata is adapted to Changing Conditions in Wastewater Treatment Plants

scientific article published on 25 April 2019

The Tubular Sheaths Encasing Methanosaeta thermophila Filaments Are Functional Amyloids.

scientific article

The activated sludge ecosystem contains a core community of abundant organisms

scientific article

The bacteriology of chronic venous leg ulcer examined by culture-independent molecular methods.

scientific article published in January 2010

The impact of immigration on microbial community composition in full-scale anaerobic digesters

scientific article published on 24 August 2017

The in situ physiology of Skermania piniformis in foams in Australian activated sludge plants.

scientific article

The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function

scientific article

The microorganisms in chronically infected end-stage and non-end-stage cystic fibrosis patients

scientific article

The novel genus, 'Candidatus Phosphoribacter', previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide

scientific article published on 25 February 2022

The proteome of Tetrasphaera elongata is adapted to changing conditions in wastewater treatment plants: Supplemental Dataset 1

article

The role of inoculum and reactor configuration for microbial community composition and dynamics in mainstream partial nitritation anammox reactors.

scientific article published on 10 March 2017

True microbiota involved in chronic lung infection of cystic fibrosis patients found by culturing and 16S rRNA gene analysis

scientific article

Use of cultivation-dependent and -independent techniques to assess contamination of central venous catheters: a pilot study

scientific article published on 28 October 2008

Variations in microcolony strength of probe-defined bacteria in activated sludge flocs

scientific article published in November 2004

Widespread abundance of functional bacterial amyloid in mycolata and other gram-positive bacteria

scientific article published on 24 April 2009

‘Candidatus Halomonas phosphatis’, a novel polyphosphate‐accumulating organism in full‐scale enhanced biological phosphorus removal plants ⬇️

scientific article published on July 25, 2012

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